Genome Info ID Organism Name RefSeq Accessions Chromosomes Plasmids Isolation Source Isolation Comments Category 40141 Acaryochloris marina MBIC11017 NC_009925,NC_009926,NC_009927,NC_009928,NC_009929,NC_009930,NC_009931,NC_009932,NC_009933,NC_009934 1 9 algae from the coast of the Palau Islands isolated from algae from the coast of the Palau Islands in the western Pacific Plant/agriculture-associated 307039 Acetobacter pasteurianus 386B NC_021991.1,NC_021993.1,NC_021978.1,NC_021979.1,NC_021977.1,NC_021976.1,NC_021992.1 1 6 spontaneous cocoa bean heap fermentation originates from a spontaneous cocoa bean heap fermentation carried out in Ghana Production-site-facility 139226 Acetobacter pasteurianus IFO 3283-01 NC_013209,NC_013210,NC_013211,NC_013212,NC_013213,NC_013214,NC_013215 1 6 pellicle on the surface of vinegar fermentation Production-site-facility 142730 Acetobacter pasteurianus IFO 3283-01-42C NC_017150,NC_017151,NC_017152,NC_017105,NC_017106,NC_017107,NC_017104 1 6 IFO 3283, was originally isolated from a pellicle (a kind of biofilm) on the surface of vinegar fermentation Obtained from IFO 3283 strain Production-site-facility 145093 Acetobacter pasteurianus IFO 3283-03 NC_017100, NC_017101,NC_017118,NC_017119,NC_017120,NC_017142,NC_017109 1 6 IFO 3283, was originally isolated from a pellicle (a kind of biofilm) on the surface of vinegar fermentation Obtained from IFO 3283 strain Production-site-facility 143188 Acetobacter pasteurianus IFO 3283-07 NC_017121,NC_017143,NC_017122,NC_017123,NC_017144,NC_017124,NC_017110 1 6 IFO 3283, was originally isolated from a pellicle (a kind of biofilm) on the surface of vinegar fermentation Production-site-facility 146001 Acetobacter pasteurianus IFO 3283-12 NC_017108,NC_017136,NC_017113,NC_017114,NC_017115,NC_017116,NC_017137 1 6 IFO 3283, was originally isolated from a pellicle (a kind of biofilm) on the surface of vinegar fermentation Production-site-facility 142344 Acetobacter pasteurianus IFO 3283-22 NC_017125,NC_017126,NC_017127,NC_017128,NC_017129,NC_017117,NC_017145 1 6 IFO 3283, was originally isolated from a pellicle (a kind of biofilm) on the surface of vinegar fermentation Obtained from IFO 3283 strain Production-site-facility 144932 Acetobacter pasteurianus IFO 3283-26 NC_017146,NC_017130,NC_017131,NC_017132,NC_017133,NC_017147,NC_017148 1 6 IFO 3283, was originally isolated from a pellicle (a kind of biofilm) on the surface of vinegar fermentation Obtained from IFO 3283 strain Production-site-facility 144801 Acetobacter pasteurianus IFO 3283-32 NC_017111,NC_017112,NC_017103,NC_017102,NC_017135,NC_017134,NC_017149 1 6 IFO 3283, was originally isolated from a pellicle (a kind of biofilm) on the surface of vinegar fermentation Obtained from IFO 3283 strain Production-site-facility 178547 Acetobacterium woodii DSM 1030 NC_016894.1 1 0 unknown 30843 Acetohalobium arabaticum DSM 5501 NC_014378 1 0 isolated from lagoons of the Arabat spit (East Crimea) which separates Sivash lake from the Sea of Azov Aquatic-environment 134690 Acholeplasma laidlawii PG-8A NC_010163 1 0 waste waters Polluted/impacted environment 160325 Achromobacter xylosoxidans A8 NC_014640,NC_014641,NC_014642 1 2 soil contaminated with polychlorinated biphenyls (PCBs) isolated from soil contaminated with polychlorinated biphenyls (PCBs) and is able to use 2-chlorobenzoate (2-CB) and 2,5-dichlorobenzoate (2,5-DCB) as sole sources of carbon and energy Polluted/impacted environment 258436 Achromobacter xylosoxidans NBRC 15126 = ATCC 27061 NC_023061.1 1 0 Lab/Engineered Achromobacter xylosoxidans NH44784-1996 NC_021285 1 0 an isolate from a cystic fibrosis patient obtained in 1996 Clinical/Human-associated 109666 Acidaminococcus fermentans DSM 20731 NC_013740 1 0 Pig gut Terrestrial-animal-associated 131990 Acidaminococcus intestini RyC-MR95 NC_016077.1 1 0 Clinical/Human-associated 34262 Acidimicrobium ferrooxidans DSM 10331 NC_013124 1 0 hot spring runoff isolated from hot spring runoff in Iceland Extreme-environment 6074 Acidiphilium cryptum JF-5 NC_009484,NC_009468,NC_009469,NC_009470,NC_009471,NC_009472,NC_009473,NC_009474,NC_009467 1 8 coal mine lake sediment isolated under iron-reducing conditions from coal mine lake sediment and is able to grow by coupling the reduction of iron to the oxidation of glucose Extreme-environment 178205 Acidiphilium multivorum NC_015186,NC_015179,NC_015178,NC_015180,NC_015181,NC_015182,NC_015187,NC_015188,NC_015189 1 8 Pyritic acid mine drainage Extreme-environment 182605 Acidithiobacillus caldus SM-1 NC_015850,NC_015854,NC_015853,NC_015852,NC_015851 1 4 Isolated from a pilot bioleaching reactor Production-site-facility 29821 Acidithiobacillus ferrooxidans ATCC 23270 NC_011761 1 0 bituminous coal mine effluent isolated from bituminous coal mine effluent Extreme-environment 6930 Acidithiobacillus ferrooxidans ATCC 53993 NC_011206 1 0 the type strain DSM 2705 derived from the type strain DSM 2705 Lab/Engineered 40988 Acidobacterium capsulatum ATCC 51196 NC_012483 1 0 acidic mine drainage isolated from acidic mine drainage in Yanahara mine, Okayama, Japan Extreme-environment 155132 Acidobacterium sp. MP5ACTX9 NC_015064,NC_015057,NC_015058,NC_015059,NC_015065,NC_015060 1 5 Extreme-environment 132453 Acidothermus cellulolyticus 11B NC_008578 1 0 Acid hot spring in Yellowstone Extreme-environment 68977 Acidovorax avenae subsp. avenae ATCC 19860 NC_015138 1 0 maize leaf isolated from maize leaf Plant/agriculture-associated 38535 Acidovorax citrulli AAC00-1 NC_008752 1 0 gold mine soil Extreme-environment 55748 Acidovorax ebreus TPSY NC_011992 1 0 Isolated from groundwater collected from the U.S. Department of Energy Integrated Field Research Challenge site at Oak Ridge, TN. Aquatic-environment 27161 Acidovorax sp. JS42 NC_008782,NC_008766,NC_008765 1 2 nitrobenzene-contaminated sediment isolated from nitrobenzene-contaminated sediment and is capable of using 2-nitrotolulene as a sole carbon and energy source Polluted/impacted environment 31444 Acidovorax sp. KKS102 NC_018708.1 1 0 isolated from a soil sample in Tokyo Soil 150852 Acinetobacter baumannii 1656-2 NC_017162, NC_017163, NC_017164 1 2 Clinical/Human-associated 111166 Acinetobacter baumannii AB0057 NC_011586,NC_011585 1 1 bloodstream infection of a patient at Walter Reed Army Medical Center isolate from a bloodstream infection of a patient at Walter Reed Army Medical Center Clinical/Human-associated 42682 Acinetobacter baumannii AB307-0294 NC_011595 1 0 the blood of a hospitalized patient isolated from the blood of a hospitalized patient in Buffalo, NY Clinical/Human-associated 103538 Acinetobacter baumannii ACICU NC_010611,NC_010606,NC_010605 1 2 outbreak isolated from an outbreak in an intensive care unit in Rome Clinical/Human-associated 103176 Acinetobacter baumannii ATCC 17978 NC_009085,NC_009084,NC_009083 1 2 case of meningitis isolated from a case of meningitis Clinical/Human-associated Acinetobacter baumannii AYE NC_010410,NC_010401,NC_010402,NC_010404,NC_010403 1 4 Human clinical isolate strain responsible for a nationwide outbreak in France in 2001. Clinical/Human-associated 235688 Acinetobacter baumannii BJAB07104 NC_021726.1,NC_021728.1,NC_021727.1 1 2 isolated from blood sample of a patient with liver cirrhosis in April 2008 and January 2007 respectively. Clinical/Human-associated 233575 Acinetobacter baumannii BJAB0715 NC_021733.1,NC_021734.1 1 1 isolated from cerebrospinal fluid (CSF) sample of a patient with cerebrospinal rhinorrhea in March 2007. Clinical/Human-associated 239774 Acinetobacter baumannii BJAB0868 NC_021729.1,NC_021730.1,NC_021731.1,NC_021732.1 1 3 ascites-isolated of a patient during March 2007 and April 2008 Clinical/Human-associated Acinetobacter baumannii D1279779 NC_020547,NC_020525 1 1 Isolated in 2009 from a bacteraemic infection of an indigenous Australian male at the Royal Darwin Hospital. Clinical/Human-associated Acinetobacter baumannii MDR-TJ NC_017847,NC_017848,NC_020524 1 2 Isolated at the Second Hospital of Tianjin Medical University, China. Clinical/Human-associated 104672 Acinetobacter baumannii MDR-ZJ06 NC_017171, NC_017172 1 1 Clinical/Human-associated 88365 Acinetobacter baumannii SDF NC_010400,NC_010395,NC_010396,NC_010398 1 3 body lice collected from homeless people living isolated from body lice collected from homeless people living in France Clinical/Human-associated 182139 Acinetobacter baumannii TCDC-AB0715 NC_017387,NC_017165, NC_017166 1 2 Clinical/Human-associated 227939 Acinetobacter baumannii TYTH-1 NC_018706 1 0 isolated in Taiwan during 2008 Clinical/Human-associated 305816 Acinetobacter baumannii ZW85-1 NC_023028.1,NC_023031.1 1 1 from diarrheal patient feces Clinical/Human-associated 168233 Acinetobacter calcoaceticus PHEA-2 NC_016603.1 1 0 Industry Wastewater Polluted/impacted environment 98416 Acinetobacter sp. ADP1 NC_005966 1 0 Isolated from Fistularia commersonii in Vietnam Aquatic-life-associated 20010 Acinetobacter sp. DR1 NC_014259 1 0 soil of a rice paddy Plant/agriculture-associated 136345 Actinobacillus pleuropneumoniae serovar 3 str. JL03 NC_010278 1 0 diseased pig lung Terrestrial-animal-associated 94089 Actinobacillus pleuropneumoniae serovar 5b str. L20 NC_009053 1 0 diseased pig lung Terrestrial-animal-associated 116979 Actinobacillus pleuropneumoniae serovar 7 str. AP76 NC_010939,NC_010941,NC_010942,NC_010940 1 3 pig lung isolated from a pig lung Terrestrial-animal-associated 117883 Actinobacillus succinogenes 130Z NC_009655 1 0 the bovine rumen Terrestrial-animal-associated 155102 Actinobacillus suis H91-0380 NC_018690.1 1 0 pig with septicemia isolated from a pig with septicemia Terrestrial-animal-associated 266597 Actinoplanes friuliensis DSM 7358 NC_022657.1 1 0 Production-site-facility 238267 Actinoplanes missouriensis 431 NC_017093.1 1 0 unknown 125489 Actinoplanes sp. N902-109 NC_021191.1 1 0 unknown 97514 Actinoplanes sp. SE50/110 NC_017803.1 1 0 unknown 80567 Actinosynnema mirum DSM 43827 NC_013093 1 0 blade of grass isolated from a blade of grass Plant/agriculture-associated 310383 Adlercreutzia equolifaciens DSM 19450 NC_022567.1 1 0 human faeces isolated from human faeces, and is able to metabolize daidzeins to equol Clinical/Human-associated 156184 Aequorivita sublithincola DSM 14238 NC_018013.1 1 0 sea water from Vestfold Hills Antarctica Extreme-environment 166521 Aerococcus urinae ACS-120-V-Col10a NC_015278 1 0 Clinical/Human-associated 266385 Aeromonas hydrophila ML09-119 NC_021290.1 1 0 disease outbreak on a commercial catfish farm, and it is representative of a clonal group of A isolate from a disease outbreak on a commercial catfish farm, and it is representative of a clonal group of A. hydrophila isolates that have been causing large-scale disease outbreaks in Alabama and Mississippi since 2009 Aquatic-life-associated 135212 Aeromonas hydrophila subsp. hydrophila ATCC 7966 NC_008570 1 0 canned milk from the United States isolated from canned milk from the United States Clinical/Human-associated 2987 Aeromonas salmonicida subsp. salmonicida A449 NC_009348,NC_004923,NC_004925,NC_004924,NC_009349,NC_009350 1 5 brown trout with furunculosis isolated from a brown trout with furunculosis Clinical/Human-associated 186715 Aeromonas veronii B565 NC_015424 1 0 aquaculture pond sediment in China Polluted/impacted environment 158134 Aggregatibacter actinomycetemcomitans ANH9381 NC_016513 1 0 Aggregatibacter actinomycetemcomitans cultivated from a subgingival plaque sample of a periodontally non-diseased subject isolated from Aggregatibacter actinomycetemcomitans cultivated from a subgingival plaque sample of a periodontally non-diseased subject Clinical/Human-associated 139153 Aggregatibacter actinomycetemcomitans D11S-1 NC_013416, NC_013438,NC_014629 1 2 subgingival plaque sample Clinical/Human-associated Aggregatibacter actinomycetemcomitans D7S-1 NC_017846 1 0 Cultured from a subgingival plaque of an African American female patient diagnosed with generalized aggressive periodontitis. Clinical/Human-associated 86045 Aggregatibacter aphrophilus NJ8700 NC_012913 1 0 oral flora of a healthy individual Clinical/Human-associated 91616 Agrobacterium fabrum str. C58 NC_003062,NC_003063,NC_003064,NC_003065 2 2 cherry tree tumor isolated from a cherry tree tumor Plant/agriculture-associated 129173 Agrobacterium radiobacter K84 NC_011985,NC_011983,NC_011994,NC_011990,NC_011987 2 3 Plant/agriculture-associated 164909 Agrobacterium sp. H13-3 NC_015183,NC_015508,NC_015184 2 1 rhizosphere of Lupinus luteus Plant/agriculture-associated 37146 Agrobacterium vitis S4 NC_011989,NC_011982,NC_011988,NC_011981,NC_011986,NC_011991,NC_011984 2 5 Plant/agriculture-associated 16855 Akkermansia muciniphila ATCC BAA-835 NC_010655 1 0 Human feces Clinical/Human-associated 124741 Alcanivorax borkumensis SK2 NC_008260 1 0 Seawater sediment sample in the Isle of Borkum, North Sea Aquatic-environment 180256 Alcanivorax dieselolei B5 NC_018691.1 1 0 oil-contaminated sea water at the Yellow River dock of Shengli oilfield Polluted/impacted environment Alicycliphilus denitrificans BC NC_014910,NC_014908,NC_014911 1 2 Isolated from a mixture of wastewater treatment plant material and benzene-polluted soil. Polluted/impacted environment 79014 Alicycliphilus denitrificans K601 NC_015422,NC_015423 1 1 a wastewater treatment plant Polluted/impacted environment 73240 Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 NC_013205,NC_013206,NC_013207,NC_013208 1 3 acidic hot spring isolated from an acidic hot spring Extreme-environment 206692 Alicyclobacillus acidocaldarius subsp. acidocaldarius Tc-4-1 NC_017167.1 1 0 hot spring in Tengchong, Yunnan, China Extreme-environment 95923 Aliivibrio salmonicida LFI1238 NC_011312,NC_011313,NC_011314,NC_011315,NC_011316,NC_011311 2 4 Atlantic cod from Hammerfest, Norway Aquatic-life-associated 145170 Alistipes finegoldii DSM 17242 NC_018011.1 1 0 Human appendix tissue Human appendix tissue Clinical/Human-associated 154597 Alistipes shahii WAL 8301 NC_021030.1 1 0 Human appendix tissue Clinical/Human-associated 114327 Alkalilimnicola ehrlichii MLHE-1 NC_008340 1 0 Mono Lake isolated from Mono Lake in California, which contains arsenic and has high pH and salt concentrations Extreme-environment 61848 Alkaliphilus metalliredigens QYMF NC_009633 1 0 Borax leachate ponds Extreme-environment 124042 Alkaliphilus oremlandii OhILAs NC_009922 1 0 Anoxic sediments from the Ohio River, Pennsylvania Aquatic-environment 64954 Allochromatium vinosum DSM 180 NC_013851,NC_013862,NC_013852 1 2 ditch water isolated from ditch water and is a model organism for studying phototrophic sulfur organization Aquatic-environment 162766 alpha proteobacterium HIMB5 NC_018643.1 1 0 Kaneohe Bay This strain was collected from Kaneohe Bay, outside the North channel. Aquatic-environment 159630 alpha proteobacterium HIMB59 NC_018644.1 1 0 collected from Kaneohe Bay, Hawaii Aquatic-environment 187312 Alteromonas macleodii AltDE1 NC_019393.1,NC_019394.1 1 1 seawater from South Adriatic Sea Aquatic-environment 281968 Alteromonas macleodii str. 'Aegean Sea MED64' NC_023045.1 1 0 coastal waters of Israel (Eastern Aegean) isolated from coastal waters of Israel (Eastern Aegean) Aquatic-environment 188897 Alteromonas macleodii str. 'Balearic Sea AD45' NC_018679.1,NC_018680.1 1 1 baltic sea Aquatic-environment 189371 Alteromonas macleodii str. 'Black Sea 11' NC_018692.1 1 0 black sea Aquatic-environment 49397 Alteromonas macleodii str. 'Deep ecotype' NC_011138 1 0 seawater obtained at a depth of 3500 meters from the Urania Basin isolated from seawater obtained at a depth of 3500 meters from the Urania Basin in the Mediterranean Sea by plating Aquatic-environment 281201 Alteromonas macleodii str. 'English Channel 615' NC_021716.1,NC_021709.1 1 1 the L4 long-term coastal monitoring station off Plymouth (English Channel) isolated on surface waters from the L4 long-term coastal monitoring station off Plymouth (English Channel) Aquatic-environment 189424 Alteromonas macleodii str. 'English Channel 673' NC_018678.1 1 0 english channel Aquatic-environment 287461 Alteromonas macleodii str. 'Ionian Sea U4' NC_021710.1,NC_021711.1 1 1 the Ionian Sea at the Uranian Basin (West of Crete) isolated from the Ionian Sea at the Uranian Basin (West of Crete) Aquatic-environment 279528 Alteromonas macleodii str. 'Ionian Sea U7' NC_021717.1 1 0 the Ionian Sea at the Uranian Basin (West of Crete) isolated from the Ionian Sea at the Uranian Basin (West of Crete) Aquatic-environment 284242 Alteromonas macleodii str. 'Ionian Sea U8' NC_021712.1 1 0 the Ionian Sea at the Uranian Basin (West of Crete) isolated from the Ionian Sea at the Uranian Basin (West of Crete) Aquatic-environment 287510 Alteromonas macleodii str. 'Ionian Sea UM4b' NC_021714.1 1 0 the Ionian Sea at the Uranian Basin (West of Crete) isolated from the Ionian Sea at the Uranian Basin (West of Crete) Aquatic-environment 281117 Alteromonas macleodii str. 'Ionian Sea UM7' NC_021713.1,NC_021718.1 1 1 the Ionian Sea at the Uranian Basin (West of Crete) isolated from the Ionian Sea at the Uranian Basin (West of Crete) Aquatic-environment 152916 Alteromonas sp. SN2 NC_015554 1 0 crude oil contaminated sea site Isolate was obtained from crude oil contaminated sea site Polluted/impacted environment 31354 Aminobacterium colombiense DSM 12261 NC_014011 1 0 Anaerobic lagoon of dairy wastewater treatment plant in Colombia Polluted/impacted environment 104956 Ammonifex degensii KC4 NC_013385,NC_013386 1 1 Neutral volcanic hot spring Extreme-environment 149409 Amphibacillus xylanus NBRC 15112 NC_018704.1 1 0 alkaline compost isolated from alkaline compost and will be used for comparative analysis Polluted/impacted environment 258726 Amycolatopsis mediterranei RB NC_022116.1 1 0 unknown 159786 Amycolatopsis mediterranei S699 NC_017186.1 1 0 soil sample from a pine arboretum, France Plant/agriculture-associated 151214 Amycolatopsis mediterranei U32 NC_014318 1 0 isolated from a colony-purified stock of CGMCC 4.5720 Aquatic-environment 230246 Amycolatopsis orientalis HCCB10007 NC_021252.1 1 0 unknown Amycolicicoccus subflavus DQS3-9A1 NC_015564,NC_015560,NC_015561 1 2 Isolated from crude oil-polluted soil in the Daqing Oilfield in China. Polluted/impacted environment 106394 Anabaena cylindrica PCC 7122 NC_019771.1,NC_019772.1,NC_019775.1,NC_019773.1,NC_019774.1,NC_020056.1,NC_020157.1 1 6 water, most likely pond Aquatic-environment 49473 Anabaena sp. 90 NC_019439.1,NC_019427.1,NC_019440.1,NC_019429.1,NC_019428.1 2 3 Lake Vesijarvi, Finland isolated from Lake Vesijarvi in Finland This organism produces 3 different microcystins (hepatotoxic heptapeptides) as well as other bioactive compounds Aquatic-environment 43351 Anabaena variabilis ATCC 29413 NC_014000,NC_007413,NC_007412,NC_007410,NC_007411 2 3 Freshwater; sewage oxidation pond Polluted/impacted environment 171334 Anaerobaculum mobile DSM 13181 NC_018024.1 1 0 Anaerobic wool-scouring wastewater treatment lagoon Anaerobic wool-scouring wastewater treatment lagoon Polluted/impacted environment 102398 Anaerococcus prevotii DSM 20548 NC_013171,NC_013164 1 1 human plasma isolated from human plasma Clinical/Human-associated 181647 Anaerolinea thermophila UNI-1 NC_014960 1 0 Thermophilic granular sludge Polluted/impacted environment 28364 Anaeromyxobacter dehalogenans 2CP-1 NC_011891 1 0 stream sediment near Lansing, Mich isolated from stream sediment near Lansing, Mich Aquatic-environment 31384 Anaeromyxobacter dehalogenans 2CP-C NC_007760 1 0 tropical soil, Cameroon, 1995 Soil 113478 Anaeromyxobacter sp. Fw109-5 NC_009675 1 0 Subsurface sediments (ca 15 m) at the ERSP-FRC, Oak Ridge, TN. Aquatic-environment 90767 Anaeromyxobacter sp. K NC_011145 1 0 Subsurface sediments (ca 15 m) at the ERSP-FRC, Oak Ridge, TN Aquatic-environment 103588 Anaplasma centrale str. Israel NC_013532 1 0 Terrestrial-animal-associated 303738 Anaplasma marginale str. Dawn NC_022760.1 1 0 blood Terrestrial-animal-associated 82315 Anaplasma marginale str. Florida NC_012026 1 0 pooled blood samples from naturally infected cattle isolated from pooled blood samples from naturally infected cattle in Florida Terrestrial-animal-associated 310000 Anaplasma marginale str. Gypsy Plains NC_022784.1 1 0 blood Terrestrial-animal-associated 46146 Anaplasma marginale str. St. Maries NC_004842 1 0 acutely infected cow from Northern Idaho and bears an msp1a genotype of JBB recovered from an acutely infected cow from Northern Idaho and bears an msp1a genotype of JBB Terrestrial-animal-associated 602 Anaplasma phagocytophilum HZ NC_007797 1 0 patient Isolated from a patient in New York, USA, in 1995 Clinical/Human-associated 241230 Anaplasma phagocytophilum str. Dog2 NC_021881.1 1 0 unknown 242654 Anaplasma phagocytophilum str. HZ2 NC_021879.1 1 0 unknown 231473 Anaplasma phagocytophilum str. JM NC_021880.1 1 0 Zapus hudsonius, MN isolated from Zapus hudsonius, MN Terrestrial-animal-associated 45531 Anoxybacillus flavithermus WK1 NC_011567 1 0 waste water drain at the Wairakei geothermal power station in New Zealand Polluted/impacted environment 85532 Aquifex aeolicus VF5 NC_000918,NC_001880 1 1 Extreme-environment 78728 Arcanobacterium haemolyticum DSM 20595 NC_014218 1 0 infections amongst American soldiers Clinical/Human-associated 209971 Arcobacter butzleri ED-1 NC_017187.1 1 0 Isolated from the electrode of an acetate-fed microbial fuel cell. Lab/Engineered 20197 Arcobacter butzleri RM4018 NC_009850 1 0 human patient with gastroenteritis isolated from a human patient with gastroenteritis Clinical/Human-associated 33843 Arcobacter nitrofigilis DSM 7299 NC_014166 1 0 roots of the marshplant Spartina alterniflora in Nova Scotia, Canada Plant/agriculture-associated 207210 Arcobacter sp. L NC_017192,NC_017193 1 1 isolated from the anode biofilm of a microbial fuel cell Lab/Engineered 98752 Aromatoleum aromaticum EbN1 NC_006513,NC_006823,NC_006824 1 2 sediment contaminated with ethylbenzene, this organism is capable of growing on crude oil, using polar aromatic compounds such as benzoate under both oxic and anoxic conditions isolated from sediment contaminated with ethylbenzene, this organism is capable of growing on crude oil, using polar aromatic compounds such as benzoate under both oxic and anoxic conditions Polluted/impacted environment 166201 Arthrobacter arilaitensis Re117 NC_014550,NC_014548,NC_014549 1 2 Reblochon cheese in France in 1998 Food-associated 67810 Arthrobacter aurescens TC1 NC_008711,NC_008713,NC_008712 1 2 South Dakota spill site soil that contained high concentrations (up to 29,000 microg/ml) of atrazine, as described isolated from a South Dakota spill site soil that contained high concentrations (up to 29,000 microg/ml) of atrazine, as described by Strong et al Polluted/impacted environment 38304 Arthrobacter chlorophenolicus A6 NC_011886,NC_011881,NC_011879 1 2 soil at Fort Collins, Colorado isolated from soil at Fort Collins, Colorado and is able to use 4-chlorophenol as a sole source of carbon and energy Soil 178037 Arthrobacter phenanthrenivorans Sphe3 NC_015145,NC_015146,NC_015147 1 2 creosote contaminated soil isolated from creosote contaminated soil in Greece Polluted/impacted environment 72239 Arthrobacter sp. FB24 NC_008537,NC_008541,NC_008538,NC_008539 1 3 soil contaminated with heavy metals and aromatic solvents isolated from soil contaminated with heavy metals and aromatic solvents Polluted/impacted environment 223462 Arthrobacter sp. Rue61a NC_018531.1,NC_018532.1,NC_009453.1 1 2 sludge of the biological wastewater treatment plant of a coal tar refining company, based on its ability to utilize quinaldine (2-methylquinoline) as source of carbon and energy isolated from sludge of the biological wastewater treatment plant of a coal tar refining company, based on its ability to utilize quinaldine (2-methylquinoline) as source of carbon and energy Polluted/impacted environment 153080 Arthrospira platensis NIES-39 NC_016640.1 1 0 Salt water, Lake Chad Aquatic-environment 136969 Aster yellows witches'-broom phytoplasma AYWB NC_007716,NC_007718,NC_007719,NC_007720,NC_007717 1 4 Collected from diseased lettuce plants in Celeryville, Ohio, in 1998. Plant/agriculture-associated 23432 Asticcacaulis excentricus CB 48 NC_014816,NC_014818,NC_014817,NC_014819 2 2 Pondwater Aquatic-environment 109073 Atopobium parvulum DSM 20469 NC_013203 1 0 the gingival crevices of the human oral cavity isolated from the gingival crevices of the human oral cavity Clinical/Human-associated 26047 Azoarcus sp. BH72 NC_008702 1 0 the roots of Kaller grass isolated from the roots of Kaller grass in the Punjab region of Pakistan Plant/agriculture-associated 172607 Azoarcus sp. KH32C NC_020516.1,NC_020548.1 1 1 agricultural field soil isolated from an agricultural field soil in Kumamoto, Japan, where paddy rice and soybean were rotationally cultivated Plant/agriculture-associated 17976 Azorhizobium caulinodans ORS 571 NC_009937 1 0 Sesbania rostrata, stem nodules Plant/agriculture-associated 214465 Azospirillum brasilense Sp245 NC_016617,NC_016594,NC_016618,NC_016595,NC_016596,NC_016619,NC_016597 1 6 roots Plant/agriculture-associated 169114 Azospirillum lipoferum 4B NC_016622,NC_016623,NC_016624,NC_016585,NC_016586,NC_016588,NC_016587 1 6 Plant/agriculture-associated 82869 Azospirillum sp. B510 NC_013854,NC_013856,NC_013857,NC_013858,NC_013859,NC_013860,NC_013855 1 6 rice isolated from rice in Japan Plant/agriculture-associated 292307 Azotobacter vinelandii CA NC_021149.1 1 0 soil Soil 290767 Azotobacter vinelandii CA6 NC_021150.1 1 0 soil Soil 72790 Azotobacter vinelandii DJ NC_012560 1 0 A. vinelandii strain DJ is a high-frequency transforming variant of A. vinelandii UW generated in 1984 through multiple rounds of transformation, using chromosomal DNAs from rifampin (rifampicin)-resistant and -sensitive strains derivative from Azotobacter vinelandii UW or CA or OP Lab/Engineered 304828 Bacillus amyloliquefaciens CC178 NC_022653.1 1 0 soil Soil 172706 Bacillus amyloliquefaciens DSM 7 NC_014551 1 0 Isolated from soil Soil 31356 Bacillus amyloliquefaciens FZB42 NC_009725 1 0 soil isolated from soil, and is a member of a group of free-living soil bacteria known to promote plant growth and suppress plant pathogens Soil Bacillus amyloliquefaciens IT-45 NC_020272,NC_020273 1 1 commercial strain used in horticulture Plant/agriculture-associated 321501 Bacillus amyloliquefaciens LFB112 NC_023073.1 1 0 Chinese herbs, Plant/agriculture-associated 188832 Bacillus amyloliquefaciens LL3 NC_017190,NC_017189 1 1 fermented food (Korean bibimbap) Food-associated 257914 Bacillus amyloliquefaciens subsp. plantarum AS43.3 NC_019842.1 1 0 isolated from a wheat head Plant/agriculture-associated Bacillus amyloliquefaciens subsp. plantarum CAU B946 NC_016784 1 0 Isolated from the rice rhizosphere. Produce plant growth promoting compounds. Plant/agriculture-associated 317943 Bacillus amyloliquefaciens subsp. plantarum NAU-B3 NC_022530.1,NC_022531.1 1 1 wheat rhizosphere in Jiangsu province, east China Plant/agriculture-associated Bacillus amyloliquefaciens subsp. plantarum UCMB5033 NC_022075 1 0 Plant/agriculture-associated 230146 Bacillus amyloliquefaciens subsp. plantarum UCMB5036 NC_020410.1 1 0 cotton plant Plant/agriculture-associated 235580 Bacillus amyloliquefaciens subsp. plantarum UCMB5113 NC_022081.1 1 0 the soil of Karpaty mountains, Ukraine isolated from the soil of Karpaty mountains, Ukraine Soil 238039 Bacillus amyloliquefaciens subsp. plantarum YAU B9601-Y2 NC_017061.1 1 0 isolated from the wheat rhizosphere in North China isolated from the wheat rhizosphere in North China Plant/agriculture-associated 189468 Bacillus amyloliquefaciens TA208 NC_017188.1 1 0 biotech unknown 213015 Bacillus amyloliquefaciens XH7 NC_017191.1 1 0 biotech unknown 234905 Bacillus amyloliquefaciens Y2 NC_017912.1 1 0 wheat rhizosphere, shows a broad suppression spectrum of pathogens and promotion of rooting and growth isolated from wheat rhizosphere, shows a broad suppression spectrum of pathogens and promotion of rooting and growth in many staple crops, vegetables and horticultural plants Plant/agriculture-associated 132916 Bacillus anthracis str. A0248 NC_012659,NC_012656,NC_012655 1 2 isolated from USAMRIID, Ohio Clinical/Human-associated 69550 Bacillus anthracis str. Ames NC_003997 1 0 isolate taken from a dead cow Terrestrial-animal-associated 112616 Bacillus anthracis str. 'Ames Ancestor' NC_007530,NC_007323,NC_007322 1 2 isolated in 1981 from a dead 14-month-old female Beefmaster heifer in Sarita, TX Terrestrial-animal-associated 127120 Bacillus anthracis str. CDC 684 NC_012581,NC_012579,NC_012577 1 2 Clinical/Human-associated 164028 Bacillus anthracis str. H9401 NC_017729.1,NC_017726.1,NC_017727.1 1 2 Korean cutaneous anthrax patient isolate from a Korean cutaneous anthrax patient Clinical/Human-associated 108183 Bacillus anthracis str. Sterne NC_005945 1 0 Clinical/Human-associated 152324 Bacillus atrophaeus 1942 NC_014639 1 0 unknown 7049 Bacillus cellulosilyticus DSM 2522 NC_014829 1 0 soil isolated from soil soil 84800 Bacillus cereus 03BB102 NC_012472,NC_012473 1 1 blood cultured from the blood of a 39 year old San Antonio, Texas welder who died as a result of a severe pneumonia thought to be caused by this microbe Clinical/Human-associated 120511 Bacillus cereus AH187 NC_011658,NC_011655,NC_011656,NC_011657,NC_011654 1 4 vomit isolated from the vomit of a person having eaten cooked rice by the Public Health Laboratory Service (PHLS), London, UK Clinical/Human-associated 122868 Bacillus cereus AH820 NC_011773,NC_011777,NC_011771,NC_011776 1 3 the periodontal pocket of a 76 year old female patient with marginal periodontitis and was further analyzed isolated in October 1995 in Akershus, Norway, from the periodontal pocket of a 76 year old female patient with marginal periodontitis and was further analyzed by Helgason et al Clinical/Human-associated 118379 Bacillus cereus ATCC 10987 NC_003909,NC_005707 1 1 isolated in Canada during a study of cheese spoilage Food-associated 54481 Bacillus cereus ATCC 14579 NC_004722,NC_004721 1 1 Food-associated 117876 Bacillus cereus B4264 NC_011725 1 0 case of fatal pneumonia isolated in 1969 from a case of fatal pneumonia in a male patient Clinical/Human-associated Bacillus cereus biovar anthracis CI NC_014335,NC_014331,NC_014332,NC_014333 1 3 Isolated from chimpanzees that had died with clinical symptoms of anthrax in Tai National Park, Cote d'Ivoire (CI) in 2001 and 2002. Terrestrial-animal-associated 95304 Bacillus cereus E33L NC_006274,NC_007103,NC_007104,NC_007105,NC_007106,NC_007107 1 5 swab of a dead zebra carcass isolated from a swab of a dead zebra carcass in April, 1996 (local ID: EB1 960419HT) Terrestrial-animal-associated 35046 Bacillus cereus F837/76 NC_016779,NC_016780,NC_016794 1 2 contaminated prostate wound Clinical/Human-associated 255427 Bacillus cereus FRI-35 NC_018491.1,NC_018493.1,NC_018499.1,NC_018494.1,NC_018492.1 1 4 Clinical/Human-associated 50903 Bacillus cereus G9842 NC_011772,NC_011774,NC_011775 1 2 stool samples from an outbreak that involved three individuals isolated from stool samples from an outbreak that involved three individuals in Nebraska (1996) Clinical/Human-associated 57418 Bacillus cereus NC7401 NC_016771.1,NC_016793.1,NC_016772.1,NC_016773.1,NC_016774.1,NC_016792.1 1 5 Clinical/Human-associated 120424 Bacillus cereus Q1 NC_011969,NC_011971,NC_011973 1 2 Isolated from a deep-subsurface oil reservoir in the Daqing oil field in northeastern China. Extreme-environment 58185 Bacillus clausii KSM-K16 NC_006582 1 0 soil soil Soil 177709 Bacillus coagulans 2-6 NC_015634 1 0 unknown Bacillus coagulans 36D1 NC_016023 1 0 mud sample in the effluent stream of Old Faithful Geyser 1 lactic-acid related Aquatic-environment 128034 Bacillus cytotoxicus NVH 391-98 NC_009674,NC_009673 1 1 Clinical/Human-associated 18977 Bacillus halodurans C-125 NC_002570 1 0 isolated in 1977 and is the most well studied alkaliphilic Bacillus organism Extreme-environment 315290 Bacillus infantis NRRL B-14911 NC_022524.1 1 0 open ocean Aquatic-environment 160447 Bacillus licheniformis 9945A NC_021362.1 1 0 soil Soil 203714 Bacillus licheniformis ATCC 14580 NC_006322 1 0 Clinical/Human-associated 1926 Bacillus licheniformis ATCC 14580 NC_006270 1 0 Clinical/Human-associated 104484 Bacillus megaterium DSM 319 NC_014103 1 0 Soil 35839 Bacillus megaterium QM B1551 NC_014019,NC_010008,NC_010010,NC_010009,NC_014031,NC_014023,NC_014025,NC_004604 1 7 isolated by Hillel Levinson at the Pioneering Research Division, Quartermaster and Engineering Center, Natick, MA and has been the strain of choice in several laboratories Soil 188594 Bacillus megaterium WSH-002 NC_017138,NC_017139,NC_017140,NC_017141 1 3 industrial strain Soil 80461 Bacillus pseudofirmus OF4 NC_013791,NC_013793,NC_013792 1 2 soil isolated from soil in New York State by alkaline enrichment cultures Extreme-environment 16546 Bacillus pumilus SAFR-032 NC_009848 1 0 the Spacecraft Assembly Facility at NASA Jet Propulsion Laboratory and produces spores highly resistant to UV radiation isolated from the Spacecraft Assembly Facility at NASA Jet Propulsion Laboratory and produces spores highly resistant to UV radiation Extreme-environment 78655 Bacillus selenitireducens MLS10 NC_014219 1 0 alkaline, hypersaline, arsenic-rich mud from Mono Lake, California isolated from alkaline, hypersaline, arsenic-rich mud from Mono Lake, California Extreme-environment 234038 Bacillus sp. JS NC_017743.1 1 0 soil isolated as a plant growth-promoting bacterium from soil in Korea Soil 259907 Bacillus subtilis BEST7613 NC_019948 1 0 Lab/Engineered 180317 Bacillus subtilis BSn5 NC_014976 1 0 Amorphophallus konjac calli tissue culture isolated from Amorphophallus konjac calli tissue culture by Professor Sun and stored in Bacillus molecular biology lab, State Key Laboratory of Agricultural Microbiology Lab/Engineered 322230 Bacillus subtilis PY79 NC_022898.1 1 0 Lab/Engineered 251826 Bacillus subtilis QB928 NC_018520.1 1 0 Lab/Engineered 97792 Bacillus subtilis subsp. natto BEST195 NC_017196,NC_017194 1 1 fermented soybeans isolated from fermented soybeans Food-associated 57968 Bacillus subtilis subsp. spizizenii str. W23 NC_014479 1 0 Lab/Engineered 204146 Bacillus subtilis subsp. spizizenii TU-B-10 NC_016047 1 0 soils collected near Nefta, Tunisia, and Death Valley National Monument, Soil 235659 Bacillus subtilis subsp. subtilis 6051-HGW NC_020507.1 1 0 Lab/Engineered 212039 Bacillus subtilis subsp. subtilis RO-NN-1 NC_017195.1 1 0 Isolated from soils originating from the Mojave Desert in Rosamond, CA. Soil 10457 Bacillus subtilis subsp. subtilis str. 168 NC_000964 1 0 X-ray irradiated strain, Marburg derived in 1947 from an X-ray irradiated strain, Marburg Lab/Engineered 287782 Bacillus subtilis subsp. subtilis str. BAB-1 NC_020832.1 1 0 freshwater Aquatic-environment 241091 Bacillus subtilis subsp. subtilis str. BSP1 NC_019896.1 1 0 Polluted/impacted environment 271089 Bacillus subtilis XF-1 NC_020244.1 1 0 the rhizosphere of Brassica rapa isolated from the rhizosphere of Brassica rapa Plant/agriculture-associated 148000 Bacillus thuringiensis BMB171 NC_014171,NC_014172 1 1 Strain BMB171 is a laboratory derivative of wild-type crystalliferous strain YBT- 1463 Lab/Engineered Bacillus thuringiensis Bt407 NC_018877,NC_018885,NC_018884,NC_018883,NC_018882,NC_018881,NC_018886,NC_018880,NC_018879,NC_018878 1 9 isolate that has been cured of the plasmid that encodes the insecticidal crystalline toxin Lab/engineered 252759 Bacillus thuringiensis HD-771 NC_018500.1,NC_018488.1,NC_018489.1,NC_018502.1,NC_018503.1,NC_018490.1,NC_018487.1,NC_018486.1,NC_018501.1 1 8 unknown 254294 Bacillus thuringiensis HD-789 NC_018508,NC_018516,NC_018509,NC_018510,NC_018517,NC_018511,NC_018512 1 6 Lab/Engineered 242010 Bacillus thuringiensis MC28 NC_018693.1,NC_018686.1,NC_018689.1,NC_018684.1,NC_018688.1,NC_018685.1,NC_018694.1,NC_018687.1 1 6 Mu Chuan virgin forest soil 155232 Bacillus thuringiensis serovar chinensis CT-43 NC_017208,NC_017202,NC_017209,NC_017203,NC_017204,NC_017210,NC_017205,NC_017211,NC_017206,NC_017207,NC_017212 1 10 china, soil soil 177620 Bacillus thuringiensis serovar finitimus YBT-020 NC_017200,NC_017201,NC_017199 1 2 unknown 119411 Bacillus thuringiensis serovar konkukian str. 97-27 NC_005957,NC_006578 1 1 case of severe human tissue necrosis which is unusual since human infections isolated from a case of severe human tissue necrosis which is unusual since human infections by this organism are rare Clinical/Human-associated 271919 Bacillus thuringiensis serovar kurstaki str. HD73 NC_020238.1,NC_020250.1,NC_020249.1,NC_020240.1,NC_020239.1,NC_020241.1,NC_020242.1,NC_020243.1 1 7 soil 269229 Bacillus thuringiensis serovar thuringiensis str. IS5056 NC_020376.1,NC_020391.1,NC_020385.1,NC_020381.1,NC_020378.1,NC_020394.1,NC_020390.1,NC_020380.1,NC_020393.1,NC_020384.1,NC_020377.1,NC_020379.1,NC_020392.1,NC_020383.1,NC_020382.1 1 14 isolated in 2005 from soil collected in Biebrza National Park (Poland) soil 63319 Bacillus thuringiensis str. Al Hakam NC_008600,NC_008598 1 1 collected in Iraq by the United Nations Special Commission Clinical/Human-associated 93926 Bacillus thuringiensis YBT-1518 NC_022873.1,NC_022882.1,NC_022874.1,NC_022875.1,NC_020124.1,NC_022877.1,NC_022876.1 1 5 soil isolated from soil and will be used for comparative analysis Soil 317218 Bacillus toyonensis BCT-7112 NC_022781.1,NC_022782.1,NC_022783.1 1 2 soil Soil 55973 Bacillus weihenstephanensis KBAB4 NC_010184,NC_010181,NC_010182,NC_010183,NC_010180 1 4 Clinical/Human-associated 168520 Bacteriovorax marinus SJ NC_016620,NC_019100 1 1 isolated from a marine environment Aquatic-environment 167533 Bacteroides fragilis 638R NC_016776 1 0 Isolated from an abdominal abscess. generated at the Institut Pasteur (Paris, France) from a Clinical/Human-associated isolate originating from Chicago, USA Clinical/Human-associated 29119 Bacteroides fragilis NCTC 9343 NC_003228,NC_006873 1 1 isolated from peritoneal infection in London Clinical/Human-associated 17906 Bacteroides fragilis YCH46 NC_006347,NC_006297 1 1 patient with septicemia isolated from a patient with septicemia in Japan Clinical/Human-associated 147569 Bacteroides helcogenes P 36-108 NC_014933 1 0 Pig faeces Terrestrial-animal-associated 140776 Bacteroides salanitronis DSM 18170 NC_015164,NC_015166,NC_015168,NC_015165 1 3 caecum of healthy chicken Terrestrial-animal-associated 70966 Bacteroides thetaiotaomicron VPI-5482 NC_004663,NC_004703 1 1 the feces of a healthy adult isolated from the feces of a healthy adult Clinical/Human-associated 85104 Bacteroides vulgatus ATCC 8482 NC_009614 1 0 Clinical/Human-associated 109951 Bacteroides xylanisolvens XB1A NC_021017 1 0 human intestine Clinical/Human-associated 204373 Bartonella australis Aust/NH1 NC_020300.1 1 0 host blood Isolated from a grey kangaroo (Macropus giganteus) Terrestrial-animal-associated 6912 Bartonella bacilliformis KC583 NC_008783 1 0 Clinical/Human-associated 149360 Bartonella clarridgeiae 73 NC_014932 1 0 scratch of cats Terrestrial-animal-associated 67450 Bartonella grahamii as4aup NC_012846,NC_012847 1 1 isolated from a wood mouse (Apodemus sylvaticus) in central Sweden Terrestrial-animal-associated 29080 Bartonella henselae str. Houston-1 NC_005956 1 0 human blood isolated from human blood in Houston Texas Clinical/Human-associated 254939 Bartonella quintana RM-11 NC_018533.1 1 0 rhesus macaque isolated from rhesus macaque Terrestrial-animal-associated 58630 Bartonella quintana str. Toulouse NC_005955 1 0 human blood isolated from human blood in Toulouse, France in 1993 Clinical/Human-associated 113218 Bartonella tribocorum CIP 105476 NC_010161,NC_010160 1 1 the blood of wild rats isolated from the blood of wild rats Terrestrial-animal-associated 209831 Bartonella vinsonii subsp. berkhoffii str. Winnie NC_020301.1 1 0 host blood Isolated from a dog (Canis lupus familiaris) Terrestrial-animal-associated 75062 Baumannia cicadellinicola str. Hc (Homalodisca coagulata) NC_007984 1 0 Insect-associated/other symbiont 73187 Bdellovibrio bacteriovorus HD100 NC_005363 1 0 Soil Soil 238888 Bdellovibrio bacteriovorus str. Tiberius NC_019567.1 1 0 River Tiber Aquatic-environment 242347 Bdellovibrio exovorus JSS NC_020813.1 1 0 Lab/Engineered 21058 Beijerinckia indica subsp. indica ATCC 9039 NC_010581,NC_010578,NC_010580 1 2 Acid Soil Extreme-environment 168934 Belliella baltica DSM 15883 NC_018010.1 1 0 surface water (5 m depth) of the central Baltic sea Aquatic-environment Beta proteobacterium CB NC_020417 1 0 Fresh water Aquatic-environment 91323 Beutenbergia cavernae DSM 12333 NC_012669 1 0 cave soil isolated from cave soil in Guangxi, China Soil 284089 Bibersteinia trehalosi USDA-ARS-USMARC-192 NC_020515.1 1 0 lung Terrestrial-animal-associated 27973 Bifidobacterium adolescentis ATCC 15703 NC_008618 1 0 Dairy Food-associated 150205 Bifidobacterium animalis subsp. animalis ATCC 25527 NC_017834.1 1 0 Dairy Food-associated 98964 Bifidobacterium animalis subsp. lactis AD011 NC_011835 1 0 Dairy Food-associated 240562 Bifidobacterium animalis subsp. lactis ATCC 27673 NC_022523.1 1 0 Dairy Food-associated 240121 Bifidobacterium animalis subsp. lactis B420 NC_017866.1 1 0 B. animalis subsp. lactis is a Gram-positive lactic acid bacterium commonly found in the gut of healthy humans, which has the ability to survive in the GIT. Clinical/Human-associated 31632 Bifidobacterium animalis subsp. lactis BB-12 NC_017214 1 0 Food-associated 235968 Bifidobacterium animalis subsp. lactis Bi-07 NC_017867.1 1 0 B. animalis subsp. lactis is a Gram-positive lactic acid bacterium commonly found in the gut of healthy humans, which has the ability to survive in the GIT. Clinical/Human-associated 84420 Bifidobacterium animalis subsp. lactis Bl-04 NC_012814 1 0 Clinical/Human-associated 289000 Bifidobacterium animalis subsp. lactis Bl12 NC_021593.1 1 0 colonoscopic sample isolated from a colonoscopic sample Clinical/Human-associated 205393 Bifidobacterium animalis subsp. lactis BLC1 NC_017216 1 0 Food-associated 208441 Bifidobacterium animalis subsp. lactis CNCM I-2494 NC_017215.1 1 0 Gantrointestinal tract Clinical/Human-associated 93544 Bifidobacterium animalis subsp. lactis DSM 10140 NC_012815 1 0 Yoghurt; Switzerland Food-associated 108068 Bifidobacterium animalis subsp. lactis V9 NC_017217 1 0 the feces of healthy Mongolian infants isolated from the feces of healthy Mongolian infants in China Clinical/Human-associated 238944 Bifidobacterium asteroides PRL2011 NC_018720.1 1 0 hindgut of Apis mellifera var. Ligustica Insect-associated/other symbiont 87902 Bifidobacterium bifidum BGN4 NC_017999.1 1 0 human feces isolated from human feces in Korea Clinical/Human-associated 153886 Bifidobacterium bifidum PRL2010 NC_014638 1 0 infant stool samples isolated from infant stool samples Clinical/Human-associated 172477 Bifidobacterium bifidum S17 NC_014616 1 0 Isolated from feces of a breast-fed infant. Clinical/Human-associated 167886 Bifidobacterium breve ACS-071-V-Sch8b NC_017218 1 0 Clinical/Human-associated 30019 Bifidobacterium breve UCC2003 NC_020517 1 0 infant nursing stool isolated from an infant nursing stool Clinical/Human-associated 66312 Bifidobacterium dentium Bd1 NC_013714 1 0 dental caries Clinical/Human-associated 134794 Bifidobacterium longum DJO10A NC_010816,NC_004252,NC_004253 1 2 Healthy young adult's fece Clinical/Human-associated 107831 Bifidobacterium longum NCC2705 NC_004307,NC_004943 1 1 infant feces isolated from infant feces Clinical/Human-associated 182273 Bifidobacterium longum subsp. infantis 157F NC_015052,NC_015053,NC_015066 1 2 faeces of a human infant Clinical/Human-associated 71229 Bifidobacterium longum subsp. infantis ATCC 15697 NC_011593 1 0 human infant feces isolated from human infant feces and will be used for comparative genomics Clinical/Human-associated 171405 Bifidobacterium longum subsp. longum BBMN68 NC_014656 1 0 long-lived man's intestinal tract isolate from long-lived man's intestinal tract Clinical/Human-associated 156230 Bifidobacterium longum subsp. longum F8 NC_021008 1 0 Clinical/Human-associated 48544 Bifidobacterium longum subsp. longum JCM 1217 NC_015067 1 0 Clinical/Human-associated 164510 Bifidobacterium longum subsp. longum JDM301 NC_014169 1 0 adult humans and formula fed infants as a normal component of gut flora Clinical/Human-associated 201753 Bifidobacterium longum subsp. longum KACC 91563 NC_017221,NC_017220,NC_017222 1 2 isolated from feces of neonates. Clinical/Human-associated 274299 Bifidobacterium thermophilum RBL67 NC_020546.1 1 0 baby feces isolated from baby feces Clinical/Human-associated 239442 Blastococcus saxobsidens DD2 NC_016943.1 1 0 isolated from below the surface of a Sardinian wall calcarenite stone sample Soil 249139 Blattabacterium sp. (Blaberus giganteus) NC_017924.1,NC_017925.1 1 1 Insect-associated/other symbiont 227520 Blattabacterium sp. (Blatta orientalis) str. Tarazona NC_020195.1,NC_020196.1 1 1 Insect-associated/other symbiont 132937 Blattabacterium sp. (Blattella germanica) str. Bge NC_013454 1 0 fat body of female adult German cockroach collected fat body of female adult German cockroach. Insect-associated/other symbiont 219128 Blattabacterium sp. (Cryptocercus punctulatus) str. Cpu NC_016598,NC_016621 1 1 Insect-associated/other symbiont 203910 Blattabacterium sp. (Mastotermes darwiniensis) str. MADAR NC_016146,NC_016150 1 1 termite Insect-associated/other symbiont 300188 Blattabacterium sp. (Nauphoeta cinerea) NC_022550.1,NC_022551.1 1 1 Insect-associated/other symbiont 281159 Blattabacterium sp. (Panesthia angustipennis spadica) str. BPAA NC_020510.1 1 0 Insect-associated/other symbiont 127104 Blattabacterium sp. (Periplaneta americana) str. BPLAN NC_013418,NC_013419 1 1 Insect-associated/other symbiont 43433 Bordetella avium 197N NC_010645 1 0 Clinical/Human-associated 30267 Bordetella bronchiseptica 253 NC_019382.1 1 0 Clinical/Human-associated 261806 Bordetella bronchiseptica MO149 NC_018829.1 1 0 Clinical/Human-associated 124907 Bordetella bronchiseptica RB50 NC_002927 1 0 rabbit isolated from a rabbit Terrestrial-animal-associated 43418 Bordetella parapertussis 12822 NC_002928 1 0 infected infant isolated from an infected infant in Germany in 1993 Clinical/Human-associated 136155 Bordetella parapertussis 18323 NC_018518.1 1 0 Clinical/Human-associated 261984 Bordetella parapertussis Bpp5 NC_018828.1,NC_018830.1 1 1 Clinical/Human-associated 192275 Bordetella pertussis CS NC_017223 1 0 Chinese pertussis vaccine strain Clinical/Human-associated 7866 Bordetella pertussis Tohama I NC_002929 1 0 patient with whooping cough and has been studied extensively for over 40 years isolated from a patient with whooping cough and has been studied extensively for over 40 years Clinical/Human-associated 31633 Bordetella petrii DSM 12804 NC_010170 1 0 river sediment isolated from river sediment Aquatic-environment 3878 Borrelia afzelii PKo NC_008277,NC_008564,NC_008565,NC_008566,NC_008567,NC_008273,NC_008568,NC_008274,NC_008569,NT_167350,NT_167351,NT_167352 1 11 human erythema migrans; Germany Clinical/Human-associated 124426 Borrelia bissettii DN127 NC_015903,NC_015921,NC_015904,NC_015905,NC_015906,NC_015907,NC_015908,NC_015909,NC_015910,NC_015911,NC_015915,NC_015916,NC_015917,NC_015918,NC_015919,NC_015920,NC_015922 1 16 western blackleg tick, Ixodes pacificus, isolated from a western blackleg tick, Ixodes pacificus, in California Insect-associated/other symbiont 75917 Borrelia burgdorferi B31 NC_001318,NC_001904,NC_001903,NC_000948,NC_000949,NC_000950,NC_000951,NC_000952,NC_000953,NC_000954,NC_000957,NC_000955,NC_000956,NC_001849,NC_001850,NC_001851,NC_001852,NC_001853,NC_001854,NC_001855,NC_001856,NC_001857 1 21 the original Lyme-disease tick isolate derived derived by limited dilutional cloning from the original Lyme-disease tick isolate derived by A. Barbour Insect-associated/other symbiont 311238 Borrelia burgdorferi CA382 NC_022048.1 1 0 Although some isolates of B. burgdorferi s.s. were cultured from woodrats, there was no clear association of this human pathogen with any vertebrate host. Terrestrial-animal-associated 89777 Borrelia burgdorferi JD1 NC_017403,NC_017395,NC_017394,NC_017427,NC_017425,NC_017426,C_017397,NC_017428,NC_017393,NC_017396,NC_017410,NC_017409,NC_017404,NC_017405,NC_017407,NC_017406,NC_017408,NC_017412,NC_017411,NC_017413,NC_013129 1 20 nymphal deer tick, Ixodes scapularis, isolated from a nymphal deer tick, Ixodes scapularis, in Ipswich, Massachusetts Insect-associated/other symbiont 74862 Borrelia burgdorferi N40 NC_017418,C_017401,NC_017400,NC_017398,NC_017422,NC_017402,NC_017424,NC_017423,NC_017399,NC_017417,NC_017420,NC_017419,NC_017416,NC_017415,NC_017414,C_017421,NC_013130 1 16 adult deer tick, Ixodes dammini, isolated from an adult deer tick, Ixodes dammini, in New York Insect-associated/other symbiont 54821 Borrelia burgdorferi ZS7 NC_011728,NC_011784,NC_011735,NC_011778,NC_011720,NC_011781,NC_011782,NC_011731,NC_011785,NC_011736,NC_011779,NC_011780,NC_011722,NC_011724,NC_011783 1 14 Clinical/Human-associated 230281 Borrelia crocidurae str. Achema NC_017808,NC_017794,NC_017774,NC_017809,NC_017775,NC_017810,NC_017776,NC_017777,NC_017811,NC_017778,NC_017779,NC_017812,NC_017780,NC_017813,NC_017781,NC_017782,NC_017814,NC_017783,NC_017784,NC_017815,NC_017785,NC_017816,NC_017795,NC_017786,NC_017817,NC_017796,NC_017818,NC_017797,NC_017798,NC_017819,NC_017799,NC_017800,NC_017787,NC_017820,NC_017788,NC_017789,NC_017821,NC_017801,NC_017802,NC_017822 1 39 tick-associated Clinical/Human-associated 9941 Borrelia duttonii Ly NC_011229,NC_011226,NC_011247,NC_011257,NC_011259,NC_011261,NC_011265,NC_011245,NC_011248,NC_011249,NC_011250,NC_011251,NC_011254,NC_011256,NC_011262,NC_011264,NC_011224 1 16 2-year-old girl with tick-borne relapsing fever isolated from a 2-year-old girl with tick-borne relapsing fever in Tanzania Clinical/Human-associated 221222 Borrelia garinii BgVir NC_017717,NC_017725,NC_017804 1 2 Isolated from an Ixodes persulcatus female Clinical/Human-associated 263154 Borrelia garinii NMJW1 NC_018747.1 1 0 tick Isolated from tick in Inner Mongolia, China Insect-associated/other symbiont 102262 Borrelia garinii PBi NC_006156,NC_006128,NC_006129,NS_000196 1 2 the cerebrospinal fluid of a patient with neuroborreliosis isolated in Germany from the cerebrospinal fluid of a patient with neuroborreliosis Clinical/Human-associated 61105 Borrelia hermsii DAH NC_010673 1 0 Blood isolated from a case of relapsing fever in western Washington Clinical/Human-associated 287661 Borrelia miyamotoi LB-2001 NC_022079.1 1 0 blood of infected SCID mice Insect-associated/other symbiont 40566 Borrelia recurrentis A1 NC_011244,NC_011252,NC_011253,NC_011255,NC_011258,NC_011260,NC_011263,NC_011246 1 7 adult patient with louse-borne relapsing fever isolated from adult patient with louse-borne relapsing fever in Ethiopia Clinical/Human-associated 92789 Borrelia turicatae 91E135 NC_008710 1 0 the soft tick Ornithodoros turicatae isolated in the United States from the soft tick Ornithodoros turicatae and will be used for comparative analysis Insect-associated/other symbiont 133938 Brachybacterium faecium DSM 4810 NC_013172 1 0 Poultry deep litter Polluted/impacted environment 62857 Brachyspira hyodysenteriae WA1 NC_012225,NC_012226 1 1 Terrestrial-animal-associated 203305 Brachyspira intermedia PWS/A NC_017243,NC_017242 1 1 weaned pigs with diarrhea, England Terrestrial-animal-associated 21074 Brachyspira murdochii DSM 12563 NC_014150 1 0 pig isolated from a pig Terrestrial-animal-associated 164347 Brachyspira pilosicoli 95/1000 NC_014330 1 0 pig isolated from a pig Terrestrial-animal-associated 234122 Brachyspira pilosicoli B2904 NC_018607.1 1 0 Terrestrial-animal-associated 201933 Brachyspira pilosicoli P43/6/78 NC_019908.1 1 0 Pig with diarrhea and colitis, Glasgow, Scotland Terrestrial-animal-associated 237679 Brachyspira pilosicoli WesB NC_018604.1 1 0 Aboriginal child Australian Aboriginal child with diarrhoea Clinical/Human-associated 65052 Bradyrhizobium japonicum USDA 110 NC_004463 1 0 Glycine hispida isolated from Glycine hispida in 1959 in Florida, USA, and has been widely studied because of its superior symbiotic nitrogen fixation with soybeans as compared to other strains Plant/agriculture-associated 202769 Bradyrhizobium japonicum USDA 6 NC_017249 1 0 isolated from nodules of a soybean planted in Japan Plant/agriculture-associated 259415 Bradyrhizobium oligotrophicum S58 NC_020453.1 1 0 paddy field soil isolated from paddy field soil Plant/agriculture-associated 29847 Bradyrhizobium sp. BTAi1 NC_009485,NC_009475 1 1 this plant at the Boyce Thompson Institute for Plant Research isolated from this plant at the Boyce Thompson Institute for Plant Research in Ithaca, NY Plant/agriculture-associated 122330 Bradyrhizobium sp. ORS278 NC_009445 1 0 Aeschynomene stem nodule isolated from an Aeschynomene stem nodule and is photosynthetic, which is a rare trait in Rhizobium bacteria Plant/agriculture-associated 65220 Bradyrhizobium sp. S23321 NC_017082.1 1 0 paddy field soil at the experimental farm of Tohoku University Plant/agriculture-associated 96763 Brevibacillus brevis NBRC 100599 NC_012491 1 0 isolated from soil Soil 37974 Brevundimonas subvibrioides ATCC 15264 NC_014375 1 0 black sand, coastline Aquatic-environment 220367 Brucella abortus A13334 NC_016777,NC_016795 2 0 fetus gastric of dairy cattle isolated from fetus gastric of dairy cattle in Yangpyeong, Korea Terrestrial-animal-associated 15061 Brucella abortus bv. 1 str. 9-941 NC_006932,NC_006933 2 0 Terrestrial-animal-associated 38055 Brucella abortus S19 NC_010742,NC_010740 2 0 spontaneously attenuated strain discovered by Dr John Buck in 1923 Clinical/Human-associated 25663 Brucella canis ATCC 23365 NC_010103,NC_010104 2 0 Allantoic fluid of aborted beagle puppy Terrestrial-animal-associated 223303 Brucella canis HSK A52141 NC_016778,NC_016796 2 0 dog blood isolated from dog blood in Hwaseong, Korea Terrestrial-animal-associated 320495 Brucella ceti TE10759-12 NC_022906.1,NC_022905.1 2 0 brain tissue Terrestrial-animal-associated Brucella ceti TE28753-12 NC_022907,NC_022908 2 0 Adriatic Sea Aquatic-environment 14466 Brucella melitensis ATCC 23457 NC_012441,NC_012442 2 0 human blood and bone marrow samples obtained from human blood and bone marrow samples Clinical/Human-associated 86222 Brucella melitensis biovar Abortus 2308 NC_007618,NC_007624 2 0 Terrestrial-animal-associated 92729 Brucella melitensis bv. 1 str. 16M NC_003317,NC_003318 2 0 infected goat isolated from an infected goat and is pathogenic in humans Terrestrial-animal-associated 176544 Brucella melitensis M28 NC_017244,NC_017245 2 0 isolated from a sheep Terrestrial-animal-associated 157313 Brucella melitensis M5-90 NC_017246,NC_017247 2 0 originated after a virulent B. melitensis strain (M28) isolated from a sheep was serially passaged through chickens, treated with acriflavine, and passaged for 90 generations in chicken embryo fibroblasts Terrestrial-animal-associated 196544 Brucella melitensis NI NC_017248,NC_017283 2 0 infected cattle isolated from the infected cattle in Inner Mongolia of China Terrestrial-animal-associated 92249 Brucella microti CCM 4915 NC_013119,NC_013118 2 0 systemically infected voles in South Moravia, Czech Republic Terrestrial-animal-associated 136990 Brucella ovis ATCC 25840 NC_009504,NC_009505 2 0 sheep tissue isolated from sheep tissue in Australia and will be used for comparative analysis with other Brucella species Terrestrial-animal-associated Brucella pinnipedialis B2/94 NC_015857,NC_015858 2 0 Isolated from marine mammals. Aquatic-life-associated 107850 Brucella suis 1330 NC_004310,NC_004311 2 0 swine A swine isolate Terrestrial-animal-associated Brucella suis 1330 NC_017251,NC_017250 2 0 Swine isolate Terrestrial-animal-associated 83806 Brucella suis ATCC 23445 NC_010169,NC_010167 2 0 Hare Terrestrial-animal-associated 219962 Brucella suis VBI22 NC_016775,NC_016797 2 0 field isolated, raw milk from an infected cow in Texas Terrestrial-animal-associated 116070 Buchnera aphidicola (Cinara tujafilina) NC_015662 1 0 Insect-associated/other symbiont 51993 Buchnera aphidicola str. 5A (Acyrthosiphon pisum) NC_011833 1 0 pea aphid, Acyrthosiphon pisum found in the pea aphid, Acyrthosiphon pisum Insect-associated/other symbiont 187588 Buchnera aphidicola str. Ak (Acyrthosiphon kondoi) NC_017256,NC_017258,NC_017257 1 2 isofemale line of Acyrthosiphon kondoi (blue alfalfa aphid) isolated from an isofemale line of Acyrthosiphon kondoi (blue alfalfa aphid) Insect-associated/other symbiont 127364 Buchnera aphidicola str. APS (Acyrthosiphon pisum) NC_002528,NC_002253,NC_002252 1 2 pea aphid, Acyrthosiphon pisum found in the pea aphid, Acyrthosiphon pisum Insect-associated/other symbiont 80364 Buchnera aphidicola str. Bp (Baizongia pistaciae) NC_004545,NC_004555 1 1 aphid, Baizongia pistaciae found in the aphid Baizongia pistaciae Insect-associated/other symbiont 7855 Buchnera aphidicola str. Cc (Cinara cedri) NC_008513,NC_011878 1 1 cedar aphid, Cinara cedri found in the cedar aphid, Cinara cedri Insect-associated/other symbiont 151781 Buchnera aphidicola str. JF98 (Acyrthosiphon pisum) NC_017254 1 0 pea aphid, Acyrthosiphon pisum found in the pea aphid, Acyrthosiphon pisum Insect-associated/other symbiont 159605 Buchnera aphidicola str. JF99 (Acyrthosiphon pisum) NC_017253 1 0 pea aphid, Acyrthosiphon pisum found in the pea aphid, Acyrthosiphon pisum Insect-associated/other symbiont 155405 Buchnera aphidicola str. LL01 (Acyrthosiphon pisum) NC_017255 1 0 pea aphid, Acyrthosiphon pisum found in the pea aphid, Acyrthosiphon pisum Insect-associated/other symbiont 100086 Buchnera aphidicola str. Sg (Schizaphis graminum) NC_004061 1 0 aphid, Schizaphis graminum symbiont of the aphid Schizaphis graminum Insect-associated/other symbiont 150843 Buchnera aphidicola str. TLW03 (Acyrthosiphon pisum) NC_017252 1 0 pea aphid, Acyrthosiphon pisum found in the pea aphid, Acyrthosiphon pisum Insect-associated/other symbiont 26317 Buchnera aphidicola str. Tuc7 (Acyrthosiphon pisum) NC_011834 1 0 aphid found in the pea aphid, Acyrthosiphon pisum Insect-associated/other symbiont 188252 Buchnera aphidicola str. Ua (Uroleucon ambrosiae) NC_017259,NC_017260,NC_017261 1 2 isofemale line of Uroleucon ambrosiae str. UA002 (brown ambrosia aphid) isolated from an isofemale line of Uroleucon ambrosiae str. UA002 (brown ambrosia aphid) Insect-associated/other symbiont 61564 Burkholderia ambifaria AMMD NC_008385,NC_008390,NC_008391,NC_008392 3 1 the rhizosphere of healthy pea plants isolated from the rhizosphere of healthy pea plants in Wisconsin, USA, in 1985 Plant/agriculture-associated 82852 Burkholderia ambifaria MC40-6 NC_010551,NC_010552,NC_010557,NC_010553 3 1 cystic fibrosis patient isolated from a cystic fibrosis patient Clinical/Human-associated 11237 Burkholderia cenocepacia AU 1054 NC_008060,NC_008061,NC_008062 3 0 the blood of a patient with CF isolated from the blood of a patient with CF Clinical/Human-associated 15205 Burkholderia cenocepacia HI2424 NC_008542,NC_008545,NC_008543,NC_008544 3 1 fields that were planted with onions samples taken from fields that were planted with onions in New York in 1999 and 2000 Plant/agriculture-associated 118154 Burkholderia cenocepacia J2315 NC_011000,NC_011001,NC_011002,NC_011003 3 1 Patient with cystic fibrosis in Edinburgh, UK Clinical/Human-associated 61509 Burkholderia cenocepacia MC0-3 NC_010508,NC_010515,NC_010512 3 0 soil associated with maize roots isolated from soil associated with maize roots Plant/agriculture-associated 187818 Burkholderia cepacia GG4 NC_018514.1,NC_018513.1 2 0 soil Soil 188977 Burkholderia gladioli BSR3 NC_015376,NC_015377,NC_015378,NC_015381,NC_015382,NC_015383 2 4 diseased rice sheath in Korea Plant/agriculture-associated 130723 Burkholderia glumae BGR1 NC_012724,NC_012721,NC_012723,NC_012718,NC_012720,NC_012725 2 4 rice isolated from rice and will be used for comparative analysis with other Burkholderia species Plant/agriculture-associated 55007 Burkholderia mallei ATCC 23344 NC_006348,NC_006349 2 0 Chinese patient came from a Chinese patient in Burma who had glanders in 1944 Clinical/Human-associated 46188 Burkholderia mallei NCTC 10229 NC_008836,NC_008835 2 0 bird Terrestrial-animal-associated 96640 Burkholderia mallei NCTC 10247 NC_009079,NC_009080 2 0 unknown 134057 Burkholderia mallei SAVP1 NC_008784,NC_008785 2 0 Terrestrial-animal-associated 17996 Burkholderia multivorans ATCC 17616 NC_010084,NC_010086,NC_010087,NC_010070 3 1 soil enriched with anthranilate at 41C Soil 203716 Burkholderia multivorans ATCC 17616 NC_010804,NC_010805,NC_010801,NC_010802 3 1 soil Soil Burkholderia phenoliruptrix BR3459a NC_018695,NC_018672,NC_018696 2 1 Isolated from a root nodule of Mimosa flocculosa, endemic to southern South America. Plant/agriculture-associated 25146 Burkholderia phymatum STM815 NC_010622,NC_010623,NC_010625,NC_010627 2 2 root nodule of Machaerium lunatum isolated from a root nodule of Machaerium lunatum in French Guiana Plant/agriculture-associated 117947 Burkholderia phytofirmans PsJN NC_010681,NC_010676,NC_010679 2 1 Surface-sterilized onion roots Plant/agriculture-associated 171872 Burkholderia pseudomallei 1026b NC_017832.1,NC_017831.1 2 0 the blood of a patient with septicemic melioidosis and has become one of the most commonly used pseudomallei Clinical/Human-associated strains isolated in Thailand in 1993 from the blood of a patient with septicemic melioidosis and has become one of the most commonly used pseudomallei Clinical/Human-associated strains in laboratory experiments Clinical/Human-associated 14980 Burkholderia pseudomallei 1106a NC_009076,NC_009078 2 0 recovered from patients presenting with recurrent melioidosis due to relapse Clinical/Human-associated 115837 Burkholderia pseudomallei 1710b NC_007434,NC_007435 2 0 recovered from patients presenting with recurrent melioidosis due to relapse Clinical/Human-associated 82117 Burkholderia pseudomallei 668 NC_009074,NC_009075 2 0 Clinical/Human-associated 252272 Burkholderia pseudomallei BPC006 NC_018529.1,NC_018527.1 2 0 Obtained from a Melioidosis Patient in Hainan, china Clinical/Human-associated 99623 Burkholderia pseudomallei K96243 NC_006350,NC_006351 2 0 Thailand isolate from Thailand Clinical/Human-associated 292259 Burkholderia pseudomallei MSHR305 NC_021877.1,NC_021884.1 2 0 autopsy brain sample Clinical/Human-associated Burkholderia pseudomallei MSHR346 NC_012695 1 0 human pathogen sputum of a melioidosis patient who was admitted to the Royal Darwin Hospital, Northern Territory, Australia in 1995 Clinical/Human-associated 263163 Burkholderia pseudomallei NCTC 13179 NC_022659.1,NC_022658.1 2 0 skin ulcer Clinical/Human-associated Burkholderia rhizoxinica HKI 454 NC_014722,NC_014718,NC_014723 1 2 intracellular symbiont of the phytopathogenic fungus Rhizopus microsporus Insect-associated/other symbiont 120713 Burkholderia sp. 383 NC_007510,NC_007511,NC_007509 3 0 Forest soil in Trinidad in 1958 Soil 1058 Burkholderia sp. CCGE1001 NC_015136,NC_015137 2 0 Rhizosphere, Rhizosphere-colonizing Plant/agriculture-associated 41388 Burkholderia sp. CCGE1002 NC_014120,NC_014117,NC_014118,NC_014119 3 1 isolated from legume nodules in Mexico and Brazil. Plant/agriculture-associated 98639 Burkholderia sp. CCGE1003 NC_014540,NC_014539 2 0 Plant/agriculture-associated 35307 Burkholderia sp. KJ006 NC_017921.1,NC_017922.1,NC_017920.1,NC_017923.1 3 1 rice root isolated from a rice root in Korea Plant/agriculture-associated 170846 Burkholderia sp. RPE64 NC_021288.1,NC_021294.1,NC_021287.1,NC_021295.1,NC_021289.1 3 2 the bean bug Riptortus pedestris isolated from the bean bug Riptortus pedestris Insect-associated/other symbiont 225579 Burkholderia sp. YI23 NC_016589,NC_016625,NC_016590,NC_016626,NC_016591,NC_016592 3 3 isolated from a golf course soil Soil 36512 Burkholderia thailandensis E264 NC_007650,NC_007651 2 0 rice field sample isolated from a rice field sample in Thailand Plant/agriculture-associated 269454 Burkholderia thailandensis MSMB121 NC_021174.1,NC_021173.1 2 0 soil Soil 89221 Burkholderia vietnamiensis G4 NC_009254,NC_009256,NC_009255,NC_009229,NC_009230,NC_009228,NC_009226,NC_009227 3 5 wastewater, Pensacola, FL Polluted/impacted environment 52548 Burkholderia xenovorans LB400 NC_007951,NC_007952,NC_007953 3 0 contaminated soil found in contaminated soil in upstate New York Polluted/impacted environment 39087 Butyrate-producing bacterium SM4/1 NC_021024 1 0 butyrate-producing bacterium SM4/1 Clinical/Human-associated 106850 Butyrate-producing bacterium SS3/4 NC_021035 1 0 butyrate-producing bacterium SS3/4 from the human intestine. Clinical/Human-associated 135163 Butyrate-producing bacterium SSC/2 NC_021016 1 0 butyrate-producing bacterium SSC/2 Clinical/Human-associated 8520 Butyrivibrio fibrisolvens NC_021031.1 1 0 Clinical/Human-associated 41874 Butyrivibrio proteoclasticus B316 NC_014388,NC_014387,NC_014390,NC_014389 2 2 isolated from the bovine rumen Terrestrial-animal-associated 135187 Caldicellulosiruptor bescii DSM 6725 NC_012034,NC_012037,NC_012036 1 2 Hot spring on the Kamchatka peninsula in Russia Extreme-environment 101559 Caldicellulosiruptor hydrothermalis 108 NC_014652 1 0 Terrestrial neutral geothermal spring; Russia, Kamchatka Extreme-environment 63887 Caldicellulosiruptor kristjanssonii 177R1B NC_014719,NC_014721 1 1 slightly alkaline hot spring isolated from a slightly alkaline hot spring in Iceland and will be used for comparative analysis with other thermophilic microorganisms Extreme-environment 6863 Caldicellulosiruptor kronotskyensis 2002 NC_014720 1 0 terrestrial neutral geothermal spring Extreme-environment 143161 Caldicellulosiruptor obsidiansis OB47 NC_014392 1 0 Obsidian Pool, Yellowstone National Park isolated from Obsidian Pool, Yellowstone National Park Extreme-environment 108203 Caldicellulosiruptor owensensis OL NC_014657 1 0 Freshwater sediment; Owens Lake, California, USA Aquatic-environment 56748 Caldicellulosiruptor saccharolyticus DSM 8903 NC_009437 1 0 hot spring isolated from a hot spring in New Zealand Extreme-environment 12258 Caldisericum exile AZM16c01 NC_017096.1 1 0 Otari Hot spring; Japan, Nagano Extreme-environment 163602 Calditerrivibrio nitroreducens DSM 19672 NC_014749,NC_014758 1 1 Terrestrial hot spring; Japan, Nagano, Yumata Extreme-environment 227687 Calothrix sp. PCC 6303 NC_019751.1,NC_019728.1,NC_019752.1,NC_019727.1 1 3 unialgal culture in lake water isolated by G C Gerloff in 1949 Aquatic-environment 15318 Calothrix sp. PCC 7507 NC_019682.1 1 0 Sphagnum bog isolated by R Ripka in 1972 Terrestrial-animal-associated 318526 Campylobacter coli 15-537360 NC_022660.1,NC_022656.1 1 1 42-year old female Clinical/Human-associated 307866 Campylobacter coli 76339 NC_022132.1 1 0 human patient with a domestically acquired infection in July 2006 Clinical/Human-associated 309484 Campylobacter coli CVM N29710 NC_022347.1,NC_022355.1,NC_022348.1 1 2 Retail meat Food-associated 95352 Campylobacter concisus 13826 NC_009802,NC_009796,NC_009795 1 2 gastrointestinal Clinical/Human-associated isolate a gastrointestinal Clinical/Human-associated isolate Clinical/Human-associated 47627 Campylobacter curvus 525.92 NC_009715 1 0 gastrointestinal Clinical/Human-associated isolate a gastrointestinal Clinical/Human-associated isolate Clinical/Human-associated 25865 Campylobacter fetus subsp. fetus 82-40 NC_008599 1 0 the blood of a human patient who was having a renal transplant isolated from the blood of a human patient who was having a renal transplant and is the best characterized isolate of this species Clinical/Human-associated 81367 Campylobacter hominis ATCC BAA-381 NC_009714,NC_009713 1 1 the feces of a healthy human isolated from the feces of a healthy human Clinical/Human-associated Campylobacter jejuni 32488 NC_021834 1 0 unknown 303321 Campylobacter jejuni 4031 NC_022529.1 1 0 Clinical/Human-associated 134361 Campylobacter jejuni RM1221 NC_003912 1 0 the skin of a retail chicken isolated from the skin of a retail chicken by the Produce Safety and Microbiology Research Unit (Western Regional Research Center, Albany, CA) and minimally passaged Food-associated 122183 Campylobacter jejuni subsp. doylei 269.97 NC_009707 1 0 Clinical/Human-associated 303969 Campylobacter jejuni subsp. jejuni 00-2425 NC_022362.1 1 0 stool sample Clinical/Human-associated 311165 Campylobacter jejuni subsp. jejuni 00-2426 NC_022352.1 1 0 stool sample Clinical/Human-associated 316167 Campylobacter jejuni subsp. jejuni 00-2538 NC_022351.1 1 0 stool sample Clinical/Human-associated 299796 Campylobacter jejuni subsp. jejuni 00-2544 NC_022353.1,NC_022354.1 1 1 stool sample Clinical/Human-associated 119085 Campylobacter jejuni subsp. jejuni 81116 NC_009839 1 0 waterborne outbreak isolated from a waterborne outbreak in 1982 and now routinely used as a laboratory strain Clinical/Human-associated 103413 Campylobacter jejuni subsp. jejuni 81-176 NC_008787,NC_008790,NC_008770 1 2 outbreak, Isolated from campylobacteriosis specimens related to consumption of raw milk at a Minnesota farm in 1985. isolated during an outbreak of campylobacteriosis in Minnesota, USA, due to the consumption of contaminated milk Clinical/Human-associated 152966 Campylobacter jejuni subsp. jejuni IA3902 NC_017279,NC_017284 1 1 aborted placenta aborted placenta of a sheep Terrestrial-animal-associated Campylobacter jejuni subsp. jejuni ICDCCJ07001 NC_014802,NC_014801 1 1 isolated from a Guillain-Barré syndrome (GBS) patient Clinical/Human-associated 14675 Campylobacter jejuni subsp. jejuni M1 NC_017280 1 0 both the patient and from the poultry flock sampled at the abattoir, thus providing a clear-cut case of the direct transmission of disease from poultry to human isolated the M1 strain (laboratory designation 99/308) from both the patient and from the poultry flock sampled at the abattoir, thus providing a clear-cut case of the direct transmission of disease from poultry to human Clinical/Human-associated 33762 Campylobacter jejuni subsp. jejuni NCTC 11168 NC_002163 1 0 diarrheic patient isolated from a diarrheic patient in 1977 and minimally passaged Clinical/Human-associated 252629 Campylobacter jejuni subsp. jejuni NCTC 11168-BN148 NC_018521.1 1 0 variant which later showed impaired colonization, invasion and motility derived from a variant which later showed impaired colonization, invasion and motility Clinical/Human-associated 247622 Campylobacter jejuni subsp. jejuni PT14 NC_018709.1 1 0 Clinical/Human-associated 157961 Campylobacter jejuni subsp. jejuni S3 NC_017281,NC_017282 1 1 the feces of a chicken, and has been shown to be non-invasive to weakly invasive isolated from the feces of a chicken, and has been shown to be non-invasive to weakly invasive in vitro Food-associated 15090 Campylobacter lari RM2100 NC_012039,NC_012040 1 1 Clinical/Human-associated 262079 Campylobacter sp. 03-427 NC_022759.1 1 0 human and reptiles isolated from human and reptiles Clinical/Human-associated 132554 Candidatus Accumulibacter phosphatis clade IIA str. UW-1 NC_013194,NC_013190,NC_013193,NC_013191 1 3 enhanced biological phosphorus removal (EBPR) wastewater treatment bioreactor Polluted/impacted environment 76781 Candidatus Amoebophilus asiaticus 5a2 NC_010830 1 0 obligate intracellular amoeba symbiont belonging to the Bacteroidetes which has been discovered within an amoeba isolated from lake sediment Insect-associated/other symbiont 203844 Candidatus Arthromitus sp. SFB-mouse-Japan NC_015913 1 0 caecal contents of SFB-gnotobiotic mice Terrestrial-animal-associated 207791 Candidatus Arthromitus sp. SFB-mouse-Yit NC_017294 1 0 Terrestrial-animal-associated 214776 Candidatus Arthromitus sp. SFB-rat-Yit NC_016012 1 0 Terrestrial-animal-associated 57536 Candidatus Azobacteroides pseudotrichonymphae genomovar. CFP2 NC_011565,NC_011562,NC_011563,NC_011564,NC_011561 1 4 single cell of the protist Pseudotrichonympha grassii which resides isolated from a single cell of the protist Pseudotrichonympha grassii which resides in the termite gut Insect-associated/other symbiont 263657 Candidatus Blochmannia chromaiodes str. 640 NC_020075.1 1 0 bacterial endosymbiont of carpenter ants collected by A. Lazarus and E. del Castillo Insect-associated/other symbiont 38691 Candidatus Blochmannia floridanus NC_005061 1 0 Insect-associated/other symbiont 110049 Candidatus Blochmannia pennsylvanicus str. BPEN NC_007292 1 0 Insect-associated/other symbiont 162273 Candidatus Blochmannia vafer str. BVAF NC_014909 1 0 Insect-associated/other symbiont 249217 Candidatus Carsonella ruddii HC isolate Thao2000 NC_018416.1 1 0 Insect-associated/other symbiont 121052 Candidatus Carsonella ruddii PV NC_008512 1 0 Insect-associated/other symbiont 183043 Candidatus Chloracidobacterium thermophilum B NC_016024,NC_016025 2 0 hot springs, Yellow Stone national park Extreme-environment 52175 Candidatus Cloacamonas acidaminovorans NC_020449.1 1 0 sludge, anaerobic mesophilic digester, municipal wastewater treatment plant Polluted/impacted environment 92303 Candidatus Desulforudis audaxviator MP104C NC_010424 1 0 Fracture water from a borehole at a depth of 2.8 km in a South African gold mine Extreme-environment 247753 Candidatus Endolissoclinum patella L2 NC_019566.1 1 0 3 m depth in a coral reef Aquatic-life-associated 112931 Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum) NC_012751,NC_012752 1 1 the pea aphid Acyrthosiphon pisum isolated from the pea aphid Acyrthosiphon pisum and will be used for comparative analysis with other insect symbionts Insect-associated/other symbiont 64223 Candidatus Hodgkinia cicadicola Dsem NC_012960 1 0 Diceroprocta semicincta collected in and around Tucson, Arizona, USA Insect-associated/other symbiont Candidatus Kinetoplastibacterium blastocrithidii (ex Strigomonas culicis) NC_019814 1 0 Insect-associated/other symbiont Candidatus Kinetoplastibacterium blastocrithidii TCC012E NC_020285 1 0 Insect-associated/other symbiont Candidatus Kinetoplastibacterium crithidii (ex Angomonas deanei ATCC 30255) NC_019815 1 0 Insect-associated/other symbiont Candidatus Kinetoplastibacterium crithidii TCC036E NC_020283 1 0 Insect-associated/other symbiont Candidatus Kinetoplastibacterium desouzaii TCC079E NC_020294 1 0 Insect-associated/other symbiont Candidatus Kinetoplastibacterium galatii TCC219 NC_020284 1 0 Insect-associated/other symbiont Candidatus Kinetoplastibacterium oncopeltii TCC290E NC_020299 1 0 Insect-associated/other symbiont 57425 Candidatus Koribacter versatilis Ellin345 NC_008009 1 0 Isolated from soil in ryegrass grass/clover pasture in Australia. soil 274386 Candidatus Liberibacter americanus str. Sao Paulo NC_022793.1 1 0 Plant/agriculture-associated 238577 Candidatus Liberibacter asiaticus str. gxpsy NC_020549.1 1 0 Insect-associated/other symbiont 64949 Candidatus Liberibacter asiaticus str. psy62 NC_012985 1 0 Diaphorina citri strain Kuwayama (Asia citrus psyllid) Insect-associated/other symbiont 97138 Candidatus Liberibacter solanacearum CLso-ZC1 NC_014774 1 0 Diaphorina citri strain Kuwayama (Asia citrus psyllid) Insect-associated/other symbiont 139927 Candidatus Methylomirabilis oxyfera NC_013260.1 1 0 Twentekanaal sediment, designated Twente, and a culture from Ooijpolder ditch sediment Aquatic-environment 156609 Candidatus Midichloria mitochondrii IricVA NC_015722 1 0 ovary of a Ixodes ricinus female adult collected near Varese - Italy Insect-associated/other symbiont 174897 Candidatus Moranella endobia PCIT NC_015735 1 0 dissected bacteriome from the mealybug Planococcus citri (Risso) isolated from a dissected bacteriome from the mealybug Planococcus citri (Risso) Insect-associated/other symbiont 259039 Candidatus Moranella endobia PCVAL NC_021057.1 1 0 Tremblaya princeps Insect-associated/other symbiont 255564 Candidatus Mycoplasma haemolamae str. Purdue NC_018219.1 1 0 Terrestrial-animal-associated 221349 Candidatus Mycoplasma haemominutum 'Birmingham 1' NC_021007.1 1 0 infected host blood Terrestrial-animal-associated 28252 Candidatus Nitrospira defluvii NC_014355 1 0 activated sludge enrichment culture Polluted/impacted environment 201843 Candidatus Pelagibacter sp. IMCC9063 NC_015380 1 0 Arctic Envirionment isolated from an Arctic Envirionment. Isolated from a surface seawater sample collected off the coastal region in Ny-Aalesund, Svalbard, Norway. Aquatic-environment 5618 Candidatus Pelagibacter ubique HTCC1062 NC_007205 1 0 Seawater samples Aquatic-environment 111091 Candidatus Phytoplasma australiense NC_010544 1 0 Saga Prefecture Japan in 1982 Plant/agriculture-associated 52977 Candidatus Phytoplasma mali NC_011047 1 0 apple tree Phytoplasma mali strain AT was collected in Heidelberg, Germany from a symptomatic apple tree Plant/agriculture-associated 26292 Candidatus Phytoplasma solani 284/09 NC_022588.1 1 0 plant tissue from tobacco and parsley samples infected with 'stolbur' strains Plant/agriculture-associated 250689 Candidatus Portiera aleyrodidarum BT-B NC_018507.1 1 0 Insect-associated/other symbiont 260212 Candidatus Portiera aleyrodidarum BT-QVLC NC_018618.1 1 0 Insect-associated/other symbiont 72727 Candidatus Protochlamydia amoebophila UWE25 NC_005861 1 0 environmental isolate Insect-associated/other symbiont 78664 Candidatus Puniceispirillum marinum IMCC1322 NC_014010 1 0 the East Sea of Korea isolated from the East Sea of Korea Aquatic-environment 232978 Candidatus Rickettsia amblyommii str. GAT-30V NC_017028.1,NC_017021.1,NC_017020.1,NC_017029.1 1 3 tick-borne Insect-associated/other symbiont 18279 Candidatus Riesia pediculicola USDA NC_014109,NC_013962 1 1 Pediculus humanus Insect-associated/other symbiont 45856 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) NC_008610 1 0 East Pacific 11 Rise, 9-N, during a December 2004 cruise Aquatic-life-associated 290995 Candidatus Saccharimonas aalborgensis NC_021219.1 1 0 metagenome an activated sludge bioreactor Polluted/impacted environment 30224 Candidatus Solibacter usitatus Ellin6076 NC_008536 1 0 rotationally grazed pasture of perennial ryegrass and white clover isolated from a rotationally grazed pasture of perennial ryegrass and white clover in Victoria, Australia Plant/agriculture-associated 150643 Candidatus Sulcia muelleri CARI NC_014499 1 0 Gut symbiont of the Blue-Green Sharpshoote Insect-associated/other symbiont 150048 Candidatus Sulcia muelleri DMIN NC_014004 1 0 bacteriome of the green sharpshooter Draeculacephala minerva Insect-associated/other symbiont 12747 Candidatus Sulcia muelleri GWSS NC_010118 1 0 Insect-associated/other symbiont 144607 Candidatus Sulcia muelleri SMDSEM NC_013123 1 0 Insect-associated/other symbiont 266476 Candidatus Tremblaya phenacola PAVE NC_021555,NC_021553 1 1 Insect-associated/other symbiont 172351 Candidatus Tremblaya princeps PCIT NC_015736 1 0 Insect-associated/other symbiont 206235 Candidatus Tremblaya princeps PCVAL NC_017293 1 0 cultivated plants in Valencia, Spain Insect-associated/other symbiont 240343 Candidatus Uzinura diaspidicola str. ASNER NC_020135.1 1 0 Insect-associated/other symbiont 128383 Candidatus Vesicomyosocius okutanii HA NC_009465 1 0 deep-sea clam, Calyptogena okutanii. collected off Hatsushima island in Sagami Bay, Japan. Aquatic-life-associated 168033 Candidatus Zinderia insecticola CARI NC_014497 1 0 Spittlebugs collected from Rosmarinus officinalis (rosemary) bushes on the University of Arizona campus Insect-associated/other symbiont 165080 Capnocytophaga canimorsus Cc5 NC_015846 1 0 Clinical/Human-associated 61160 Capnocytophaga ochracea DSM 7271 NC_013162 1 0 the human oral cavity isolated from the human oral cavity Clinical/Human-associated 26463 Carboxydothermus hydrogenoformans Z-2901 NC_007503 1 0 hot swamp from Kunashir Island, Russia isolated from a hot swamp from Kunashir Island, Russia Extreme-environment 261036 Carnobacterium maltaromaticum LMA28 NC_019425.1 1 0 Isolated from a soft ripened cheese. Food-associated 108130 Carnobacterium sp. 17-4 NC_015391,NC_015390 1 1 seawater from Isfjord, Spitsbergen, Norway Aquatic-environment 264223 Carnobacterium sp. WN1359 NC_022606.1,NC_022602.1,NC_022601.1,NC_022607.1,NC_022603.1,NC_022608.1 1 5 Siberian permafrost Isolated from Siberian permafrost, was capable of growth under a combination of low-temperature (0¿¿¿¿C), low-pressure (0 Extreme-environment 36872 Catenulispora acidiphila DSM 44928 NC_013131 1 0 Forest soil from Gerenzano italy soil 124313 Caulobacter crescentus CB15 NC_002696 1 0 Pond water Aquatic-environment 52860 Caulobacter crescentus NA1000 NC_011916 1 0 variant of wild-type strain CB15 Lab/Engineered 118057 Caulobacter segnis ATCC 21756 NC_014100 1 0 soil soil 18104 Caulobacter sp. K31 NC_010338,NC_010335,NC_010333 1 2 low-oxygen groundwater sample isolated from a low-oxygen groundwater sample and is being sequenced for comparative genome analysis Extreme-environment 18861 Cellulomonas fimi ATCC 484 NC_015514 1 0 soil soil 99035 Cellulomonas flavigena DSM 20109 NC_014151 1 0 Soil soil 158510 Cellulophaga algicola DSM 14237 NC_014934 1 0 surfaces of algal species from the Eastern Antarctic coastal zone Plant/agriculture-associated 164863 Cellulophaga lytica DSM 7489 NC_015167 1 0 Beach mud; Limon, Costa Rica Aquatic-environment 11216 Cellvibrio gilvus ATCC 13127 NC_015671 1 0 bovine feces Terrestrial-animal-associated 122165 Cellvibrio japonicus Ueda107 NC_010995 1 0 field soil isolated from field soil in Japan soil 231992 Chamaesiphon minutus PCC 6605 NC_019697.1,NC_020053.1,NC_019698.1 1 2 freshwater isolated by MM Allen Aquatic-environment 72577 Chelativorans sp. BNC1 NC_008242,NC_008254,NC_008243,NC_008244 1 3 mixed-culture enriched from sewage using the chelating agent EDTA (binds divalent cations - ethylenediamine tetraacetic acid) as the sole carbon and nitrogen source isolated from a mixed-culture enriched from sewage using the chelating agent EDTA (binds divalent cations - ethylenediamine tetraacetic acid) as the sole carbon and nitrogen source Polluted/impacted environment 99107 Chitinophaga pinensis DSM 2588 NC_013132 1 0 pine litter isolated from pine litter in Australia Plant/agriculture-associated 19118 Chlamydia muridarum Nigg NC_002620,NC_002182 1 1 isolated from a human case of respiratory tract infection Clinical/Human-associated 261150 Chlamydia pecorum P787 NC_022441.1 1 0 the synovial fluid of a sheep with arthritis isolated from the synovial fluid of a sheep with arthritis Terrestrial-animal-associated 259600 Chlamydia pecorum PV3056/3 NC_022439.1 1 0 the cervical swab of a cow with metritis isolated from the cervical swab of a cow with metritis Terrestrial-animal-associated 260990 Chlamydia pecorum W73 NC_022440.1 1 0 the feces of a healthy sheep isolated from the feces of a healthy sheep Terrestrial-animal-associated 259794 Chlamydia psittaci 01DC12 NC_019391.1,NC_019392.1 1 1 pig from Saxony-Anhalt, Germany isolated from a pig from Saxony-Anhalt, Germany Terrestrial-animal-associated 256362 Chlamydia psittaci 84/55 NC_018619.1,NC_018633.1 1 1 lungs of a diseased parakeet Terrestrial-animal-associated 211843 Chlamydia psittaci CP3 NC_018625.1,NC_018634.1 1 1 Pigeon Terrestrial-animal-associated 257067 Chlamydia psittaci GR9 NC_018620.1 1 0 duck Terrestrial-animal-associated 256934 Chlamydia psittaci M56 NC_018623.1,NC_018635.1 1 1 muskrat Terrestrial-animal-associated 255879 Chlamydia psittaci MN NC_018627.1,NC_018636.1 1 1 human throat washings Clinical/Human-associated 205346 Chlamydia psittaci NJ1 NC_018626.1,NC_018637.1 1 1 Turkey Terrestrial-animal-associated 255666 Chlamydia psittaci VS225 NC_018621.1,NC_018638.1 1 1 orange fronted parakeet Terrestrial-animal-associated 254067 Chlamydia psittaci WC NC_018624.1,NC_018639.1 1 1 cow Terrestrial-animal-associated 251844 Chlamydia psittaci WS/RT/E30 NC_018622.1,NC_018640.1 1 1 duck with no clinical signs Terrestrial-animal-associated 32542 Chlamydia trachomatis 434/Bu NC_010287 1 0 bubo Clinical/Human-associated 234016 Chlamydia trachomatis A/363 NC_020966,NC_019272 1 1 Clinical/Human-associated 230012 Chlamydia trachomatis A/5291 NC_020939,NC_020946 1 1 Clinical/Human-associated 31516 Chlamydia trachomatis A/HAR-13 NC_007429,NC_007430 1 1 conjunctiva isolate Clinical/Human-associated 93337 Chlamydia trachomatis A2497 NC_017437,NC_017438 1 1 2.5-year-old with intense active trachoma in Tanzania. Clinical/Human-associated 100303 Chlamydia trachomatis B/Jali20/OT NC_012686 1 0 the conjunctiva isolated from the conjunctiva in an active case of trachoma Clinical/Human-associated 130039 Chlamydia trachomatis B/TZ1A828/OT NC_012687 1 0 ocular isolate Clinical/Human-associated 319870 Chlamydia trachomatis C/TW-3 NC_023060.1,NC_023057.1 1 1 Clinical/Human-associated 235735 Chlamydia trachomatis D/SotonD1 NC_020967,NC_020986 1 1 UK Endocervix Clinical/Human-associated 227202 Chlamydia trachomatis D/SotonD5 NC_020943,NC_020958 1 1 UK Endocervix Clinical/Human-associated 235313 Chlamydia trachomatis D/SotonD6 NC_020968,NC_020959 1 1 UK Endocervix Clinical/Human-associated 43535 Chlamydia trachomatis D/UW-3/CX NC_000117 1 0 USA Cervix Clinical/Human-associated 153166 Chlamydia trachomatis D-EC NC_017434,NC_017435 1 1 mice Terrestrial-animal-associated 159408 Chlamydia trachomatis D-LC NC_017436,NC_017433 1 1 mice Terrestrial-animal-associated 155662 Chlamydia trachomatis E/11023 NC_017431 1 0 Clinical/Human-associated isolate Chlamydia trachomatis E/11023 is a Clinical/Human-associated isolate, cervix Clinical/Human-associated 147145 Chlamydia trachomatis E/150 NC_017439.1 1 0 Clinical/Human-associated isolate Chlamydia trachomatis E/150 is a Clinical/Human-associated isolate, rectum Clinical/Human-associated 135580 Chlamydia trachomatis E/Bour NC_020971, NC_020947 1 1 California Ocular Clinical/Human-associated 232143 Chlamydia trachomatis E/C599 NC_022537.1 1 0 was obtained from a 26-year-old asymptomatic male Clinical/Human-associated 230922 Chlamydia trachomatis E/SotonE4 NC_020969,NC_020987 1 1 UK Endocervix Clinical/Human-associated 227957 Chlamydia trachomatis E/SotonE8 NC_020942,NC_020960 1 1 UK Endocervix Clinical/Human-associated 231734 Chlamydia trachomatis E/SW3 NC_017952.1 1 0 Sweden Cervix Clinical/Human-associated 233275 Chlamydia trachomatis F/SotonF3 NC_020964,NC_020988 1 1 Clinical/Human-associated 237003 Chlamydia trachomatis F/SW4 NC_017951.1 1 0 Sweden Cervix Clinical/Human-associated 232795 Chlamydia trachomatis F/SW5 NC_017953.1 1 0 Sweden Cervix Clinical/Human-associated 233204 Chlamydia trachomatis F/SWFPminus NC_022548.1 1 0 Clinical/Human-associated 152824 Chlamydia trachomatis G/11074 NC_017440.1 1 0 Clinical/Human-associated isolate Chlamydia trachomatis G/11074 is a Clinical/Human-associated isolat Clinical/Human-associated 151128 Chlamydia trachomatis G/11222 NC_017430.1 1 0 Clinical/Human-associated isolate Chlamydia trachomatis G/11222 is a Clinical/Human-associated isolate Clinical/Human-associated 152579 Chlamydia trachomatis G/9301 NC_017432.1 1 0 Clinical/Human-associated isolate Clinical/Human-associated 149848 Chlamydia trachomatis G/9768 NC_017429 1 0 Clinical/Human-associated isolate Chlamydia trachomatis G/9768 is a Clinical/Human-associated isolate Clinical/Human-associated 240482 Chlamydia trachomatis G/SotonG1 NC_020941,NC_020961 1 1 UK Endocervix Clinical/Human-associated 235039 Chlamydia trachomatis Ia/SotonIa1 NC_020970,NC_020962 1 1 UK Endocervix Clinical/Human-associated 231702 Chlamydia trachomatis Ia/SotonIa3 NC_020940,NC_020989 1 1 UK Endocervix Clinical/Human-associated 265301 Chlamydia trachomatis IU824 NC_020511.1,NC_020551.1 1 1 Clinical/Human-associated 276860 Chlamydia trachomatis IU888 NC_020512.1,NC_020513.1 1 1 Clinical/Human-associated 172615 Chlamydia trachomatis J/6276tet1 NC_021892.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 228748 Chlamydia trachomatis K/SotonK1 NC_020965,NC_020963 1 1 UK Endocervix Clinical/Human-associated 240339 Chlamydia trachomatis L1/115 NC_020929,NC_020951 1 1 LGV patient Clinical/Human-associated 235691 Chlamydia trachomatis L1/224 NC_020973,NC_020952 1 1 LGV patient Clinical/Human-associated 210695 Chlamydia trachomatis L1/440/LN NC_020937 1 0 Lymph node Clinical/Human-associated 232811 Chlamydia trachomatis L2/25667R NC_020930 1 0 rectal biosy Clinical/Human-associated 295928 Chlamydia trachomatis L2/434/Bu(f) NC_021052.1,NC_021049.1 1 1 final stage after Lab/Engineered 292446 Chlamydia trachomatis L2/434/Bu(i) NC_021050.1,NC_021051.1 1 1 strains in the initial stage of the evolution Clinical/Human-associated 230570 Chlamydia trachomatis L2b/795 NC_020938,NC_020983 1 1 rectum Clinical/Human-associated 234903 Chlamydia trachomatis L2b/8200/07 NC_020945,NC_020984 1 1 sweden rectum Clinical/Human-associated 237967 Chlamydia trachomatis L2b/Ams1 NC_020933,NC_020980 1 1 penileulcer Clinical/Human-associated 229851 Chlamydia trachomatis L2b/Ams2 NC_020934,NC_020948 1 1 netherlands anus Clinical/Human-associated 231044 Chlamydia trachomatis L2b/Ams3 NC_020977,NC_020949 1 1 anus Clinical/Human-associated 234047 Chlamydia trachomatis L2b/Ams4 NC_020978,NC_020981 1 1 anus Clinical/Human-associated 229252 Chlamydia trachomatis L2b/Ams5 NC_020936,NC_020950 1 1 anus Clinical/Human-associated 239245 Chlamydia trachomatis L2b/Canada1 NC_020935,NC_020953 1 1 rectum Clinical/Human-associated 228272 Chlamydia trachomatis L2b/Canada2 NC_020932,NC_020954 1 1 Clinical/Human-associated 231989 Chlamydia trachomatis L2b/CV204 NC_020976,NC_020955 1 1 france rectum Clinical/Human-associated 230686 Chlamydia trachomatis L2b/LST NC_020975,NC_020985 1 1 Clinical/Human-associated 68089 Chlamydia trachomatis L2b/UCH-1/proctitis NC_010280 1 0 recent outbreak of proctitis isolated from a recent outbreak of proctitis in Europé. rectal swab of a 49-yr-old MSM who was HIV positive and Hepatitis C negative Clinical/Human-associated 228626 Chlamydia trachomatis L2b/UCH-2 NC_020931,C_020956 1 1 Clinical/Human-associated 173188 Chlamydia trachomatis L2c NC_015744 1 0 man with severe proctitis isolated from a man with severe proctitis Clinical/Human-associated 235627 Chlamydia trachomatis L3/404/LN NC_020974,NC_020957 1 1 Clinical/Human-associated 174652 Chlamydia trachomatis RC-F(s)/342 NC_021890.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 169262 Chlamydia trachomatis RC-F(s)/852 NC_021888.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 171151 Chlamydia trachomatis RC-F/69 NC_021895.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 172322 Chlamydia trachomatis RC-J(s)/122 NC_021891.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 173461 Chlamydia trachomatis RC-J/943 NC_021896.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 171008 Chlamydia trachomatis RC-J/953 NC_021889.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 172401 Chlamydia trachomatis RC-J/966 NC_021898.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 187813 Chlamydia trachomatis RC-J/971 NC_021899.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 173008 Chlamydia trachomatis RC-L2(s)/3 NC_021897.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 173773 Chlamydia trachomatis RC-L2(s)/46 NC_021887.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 189024 Chlamydia trachomatis RC-L2/55 NC_021893.1 1 0 in vitro strains were grown in McCoy cells Lab/Engineered 129597 Chlamydia trachomatis Sweden2 NC_017441 1 0 urethral sample from a Swedish man Isolated in McCoy cells in October 2006 from a urethral sample from a Swedish man, suffering from symptomatic chlamydial urethritis. Clinical/Human-associated 21869 Chlamydophila abortus S26/3 NC_004552 1 0 enzootic (affecting animals isolated from an enzootic (affecting animals in a specific geographical area) abortion case in sheep Terrestrial-animal-associated 107360 Chlamydophila caviae GPIC NC_003361,NC_004720 1 1 Terrestrial-animal-associated 51660 Chlamydophila felis Fe/C-56 NC_007899,NC_007900 1 1 cat with conjunctivitis isolated from a cat with conjunctivitis Terrestrial-animal-associated 99706 Chlamydophila pecorum E58 NC_015408 1 0 Terrestrial-animal-associated 27823 Chlamydophila pneumoniae AR39 NC_002180 1 0 University of Washington student with acute respiratory (=AR) tract infection Isolated from a University of Washington student with acute respiratory (=AR) tract infection in 1983, and epidemiologically distinct from Chlamydophila pneumoniae strain CWL029 Clinical/Human-associated 119813 Chlamydophila pneumoniae CWL029 NC_000922 1 0 Isolated in the USA before 1987 and epidemiologically distinct from Chlamydophila pneumoniae strain AR39 Clinical/Human-associated 5522 Chlamydophila pneumoniae J138 NC_002491 1 0 the pharyngeal mucosa of a 5 year old male patient with acute bronchitis Isolated in Japan in 1994 from the pharyngeal mucosa of a 5 year old male patient with acute bronchitis Clinical/Human-associated 19997 Chlamydophila pneumoniae LPCoLN NC_017285.1,NC_017286.1 1 1 originally isolated from a nasal swab of a captive koala showing signs of respiratory illness Terrestrial-animal-associated 35719 Chlamydophila pneumoniae TW-183 NC_005043 1 0 child's conjunctiva (the membranes lining the eyelid) during a trachoma vaccine trial isolated in 1965 from a child's conjunctiva (the membranes lining the eyelid) during a trachoma vaccine trial in Taiwan Clinical/Human-associated 189783 Chlamydophila psittaci 01DC11 NC_017289.1 1 0 isolated from pigs Terrestrial-animal-associated 190769 Chlamydophila psittaci 02DC15 NC_017292.1 1 0 cattle Terrestrial-animal-associated 195541 Chlamydophila psittaci 08DC60 NC_017290.1 1 0 isolated from human Clinical/Human-associated 52874 Chlamydophila psittaci 6BC NC_015217,NC_015470 1 1 avian isolate Terrestrial-animal-associated 203718 Chlamydophila psittaci 6BC NC_017287.1,NC_017288.1 1 1 isolated from a parrot during the 1929-1930 psittacosis pandemic Terrestrial-animal-associated 191677 Chlamydophila psittaci C19/98 NC_017291.1 1 0 isolated from sheep Terrestrial-animal-associated 34415 Chlamydophila psittaci Mat116 NC_020248.1 1 0 psittacosis outbreak Clinical/Human-associated 178363 Chlamydophila psittaci RD1 NC_014796.1,NC_014797.1 1 1 isolated from a mixed culture with Chlamydia trachomatis serovar L2b unknown 72705 Chlorobaculum parvum NCIB 8327 NC_011027 1 0 Aquatic-environment 46571 Chlorobium chlorochromatii CaD3 NC_007514 1 0 freshwater lake isolated from a phototrophic consortia obtained from a freshwater lake in Germany Aquatic-environment 118737 Chlorobium limicola DSM 245 NC_010803 1 0 Gilroy Hot Spring Extreme-environment 1287 Chlorobium luteolum DSM 273 NC_007512 1 0 lake polden, norway Aquatic-environment 121022 Chlorobium phaeobacteroides BS1 NC_010831 1 0 black sea Aquatic-environment 122104 Chlorobium phaeobacteroides DSM 266 NC_008639 1 0 lake isolated from a lake in Norway Aquatic-environment 132153 Chlorobium phaeovibrioides DSM 265 NC_009337 1 0 saline interine flat Aquatic-environment 116050 Chlorobium tepidum TLS NC_002932 1 0 New Zealand high-sulfide hot spring isolated from a New Zealand high-sulfide hot spring Extreme-environment 85409 Chloroflexus aggregans DSM 9485 NC_011831 1 0 Hot spring in Japan Extreme-environment 28763 Chloroflexus aurantiacus J-10-fl NC_010175 1 0 the Hakone hot spring area isolated from the Hakone hot spring area in Japan and will be used for comparative analysis Extreme-environment 61043 Chloroflexus sp. Y-400-fl NC_012032 1 0 alkaline hot spring isolated from an alkaline hot spring and will be used for comparative analysis Extreme-environment 99257 Chloroherpeton thalassium ATCC 35110 NC_011026 1 0 Marine source Aquatic-environment 67196 Chromobacterium violaceum ATCC 12472 NC_005085 1 0 freshwater isolated from freshwater in Malaya Aquatic-environment 113723 Chromohalobacter salexigens DSM 3043 NC_007963 1 0 solar salt facility on Bonaire Island, Netherlands Antilles isolated from a solar salt facility on Bonaire Island, Netherlands Antilles Extreme-environment 68870 Chroococcidiopsis thermalis PCC 7203 NC_019695.1,NC_019699.1,NC_019696.1 1 2 soil sample, near Greifswald, East Germany soil soil 288481 Chthonomonas calidirosea T49 NC_021487.1 1 0 geothermally heated soils isolated from geothermally heated soils in New Zealand Extreme-environment 71230 Citrobacter koseri ATCC BAA-895 NC_009792,NC_009794,NC_009793 1 2 human infant isolate from a human infant Clinical/Human-associated 33214 Citrobacter rodentium ICC168 NC_013716,NC_013718,NC_013719,NC_013717 1 3 Terrestrial-animal-associated 82482 Clavibacter michiganensis subsp. michiganensis NCPPB 382 NC_009480,NC_009478,NC_009479 1 2 Plant/agriculture-associated 234710 Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 NC_020891.1 1 0 maize Plant/agriculture-associated 4666 Clavibacter michiganensis subsp. sepedonicus NC_010407,NC_010408,NC_010399 1 2 Plant/agriculture-associated 152872 Clostridiales genomosp. BVAB3 str. UPII9-5 NC_013895 1 0 Endometrium; Fasidious bacterium that is highly specific for BV; human urogenital tract, associated with bacterial vaginosis Clinical/Human-associated 74127 Clostridium acetobutylicum ATCC 824 NC_003030,NC_001988 1 1 garden soil isolated in 1924 from garden soil in Connecticut, USA, by E. Wyer and L. Rettger soil 182280 Clostridium acetobutylicum DSM 1731 NC_015687,NC_015686,NC_015688 1 2 obtained from the German Collection of Microorganisms and Cell Cultures unknown 167171 Clostridium acetobutylicum EA 2018 NC_017295,NC_017296 1 1 isolated from soil Isolated from china and mutagenesis done using NTG (N-methyl-N-nitro-N-nitrosoguanidine) soil 240183 Clostridium acidurici 9a NC_018664.1,NC_018657.1 1 1 almost every soil but can also be found isolated from almost every soil but can also be found in the intestinal tract of birds soil 69853 Clostridium beijerinckii NCIMB 8052 NC_009617 1 0 Lab/Engineered 110701 Clostridium botulinum A str. ATCC 19397 NC_009697 1 0 Clinical/Human-associated 22612 Clostridium botulinum A str. ATCC 3502 NC_009495,NC_009496 1 1 Clinical/Human-associated 19727 Clostridium botulinum A str. Hall NC_009698 1 0 Clinical/Human-associated 91161 Clostridium botulinum A2 str. Kyoto NC_012563 1 0 case of infant botulism isolated from a case of infant botulism in Kyoto, Japan in 1978 and will be use for comparative analysis with other C. botulinum strains Clinical/Human-associated 822 Clostridium botulinum A3 str. Loch Maree NC_010520,NC_010418 1 1 duck liver paste during a botulism outbreak at a hotel isolated from duck liver paste during a botulism outbreak at a hotel in the Scottish highlands in 1922 Clinical/Human-associated 123574 Clostridium botulinum B str. Eklund 17B NC_010674,NC_010680 1 1 marine sediments taken off the coast of Washington, USA and was not associated with botulism isolated from marine sediments taken off the coast of Washington, USA and was not associated with botulism Aquatic-environment 127283 Clostridium botulinum B1 str. Okra NC_010516,NC_010379 1 1 Clinical/Human-associated 19908 Clostridium botulinum Ba4 str. 657 NC_012658,NC_012657,NC_012654 1 2 infant botulism case isolated from an infant botulism case in 1976 Clinical/Human-associated 178872 Clostridium botulinum BKT015925 NC_015419,NC_015425,NC_015427,NC_015426,NC_015417,NC_015418 1 5 strain from physiological group III, causing animal botulism Terrestrial-animal-associated 115804 Clostridium botulinum E3 str. Alaska E43 NC_010723 1 0 salmon eggs associated with a foodborne case of botulism isolated from salmon eggs associated with a foodborne case of botulism in Alaska, however the exact details are not available Terrestrial-animal-associated 152196 Clostridium botulinum F str. 230613 NC_017297,NC_017298 1 1 Clinical/Human-associated 15611 Clostridium botulinum F str. Langeland NC_009699,NC_009700 1 1 home-prepared liver paste Clostridium botulinum F strain Langeland was identified in 1958 from home-prepared liver paste involved in an outbreak of foodborne botulism on the island of Langeland, in Denmark. Clinical/Human-associated 180836 Clostridium botulinum H04402 065 NC_017299 1 0 isolated from a botulism patient Clinical/Human-associated 57783 Clostridium cellulolyticum H10 NC_011898 1 0 decayed grass compost Plant/agriculture-associated Clostridium cellulovorans 743B NC_014393 1 0 Woody biomass digester nitrogen fixation Production-site-facility 158569 Clostridium cf. saccharolyticum K10 NC_021047 1 0 Clinical/Human-associated 155345 Clostridium clariflavum DSM 19732 NC_016627 1 0 Methanogenic sludge of a cellulose-degrading bioreactor Polluted/impacted environment 155785 Clostridium difficile 2007855 NC_017178.1 1 0 bovine isolated in the United States in 2007 Terrestrial-animal-associated 38397 Clostridium difficile 630 NC_009089,NC_008226 1 1 Clinical/Human-associated 155290 Clostridium difficile BI1 NC_017179,NC_017177,NC_017176 1 2 human human strain isolated in the United States in 1988 Clinical/Human-associated 125228 Clostridium difficile CD196 NC_013315 1 0 single patient with a C. difficile infection isolated from a single patient with a C. difficile infection in a hospital in Paris in 1985 Clinical/Human-associated 157887 Clostridium difficile M68 NC_017175.1 1 0 human human strain isolated in Ireland in 2006 Clinical/Human-associated 78408 Clostridium difficile R20291 NC_013316 1 0 isolated in Stoke Mandeville Hospital, UK in 2006 and is closely related to the North American hypervirulent BI strains Clinical/Human-associated 111549 Clostridium kluyveri DSM 555 NC_009706,NC_009466 1 1 Mud of a canal in Delft, The Netherlands Aquatic-environment 118830 Clostridium kluyveri NBRC 12016 NC_011837,NC_011836 1 1 Mud of a canal in Delft, The Netherlands Aquatic-environment 82977 Clostridium ljungdahlii DSM 13528 NC_014328 1 0 chicken yard waste isolated from chicken yard waste and is studied for its ability to produce ethanol Polluted/impacted environment 112828 Clostridium novyi NT NC_008593 1 0 Lab/Engineered 18034 Clostridium pasteurianum BC1 NC_021182.1,NC_021183.1 1 1 coal-cleaning residues isolated from coal-cleaning residues Polluted/impacted environment 106549 Clostridium perfringens ATCC 13124 NC_008261 1 0 isolated from a human gas gangrene patient Clinical/Human-associated 122123 Clostridium perfringens SM101 NC_008262,NC_008264,NC_008263 1 2 Clinical/Human-associated 59675 Clostridium perfringens str. 13 NC_003366,NC_003042 1 1 the soil isolate from the soil soil 16213 Clostridium phytofermentans ISDg NC_010001 1 0 forest soil near the Quabbin Reservoir isolated from forest soil near the Quabbin Reservoir in Massachusetts soil 315486 Clostridium saccharobutylicum DSM 13864 NC_022571.1 1 0 soya bean field Plant/agriculture-associated 91065 Clostridium saccharolyticum WM1 NC_014376 1 0 Sewage sludge, Ottawa, Canada Polluted/impacted environment 181665 Clostridium saccharoperbutylacetonicum N1-4(HMT) NC_020291.1,NC_020292.1 1 1 derived from existing strain (derived from ATCC 13564) Lab/Engineered 224589 Clostridium sp. BNL1100 NC_016791.1 1 0 solated from Corn Stover Plant/agriculture-associated 207529 Clostridium sp. SY8519 NC_015737 1 0 Adult Human Intestine Clinical/Human-associated 275516 Clostridium stercorarium subsp. stercorarium DSM 8532 NC_020134.1 1 0 self-heated compost isolated from self-heated compost Plant/agriculture-associated 32817 Clostridium sticklandii DSM 519 NC_014614 1 0 Mud water Aquatic-environment 101274 Clostridium tetani E88 NC_004557,NC_004565 1 1 Clinical/Human-associated 47081 Clostridium thermocellum ATCC 27405 NC_009012 1 0 Yellowstone National Park Extreme-environment 140364 Clostridium thermocellum DSM 1313 NC_017304 1 0 Evolved mixed population unknown 187779 Collimonas fungivorans Ter331 NC_015856 1 0 slightly acidic dune soils in the Netherlands soil 94388 Colwellia psychrerythraea 34H NC_003910 1 0 Arctic marine sediments isolated from Arctic marine sediments Aquatic-environment 153857 Comamonas testosteroni CNB-1 NC_013446,NC_010935 1 1 activated sludge from a chemical plant isolated from activated sludge from a chemical plant Polluted/impacted environment 21639 Conexibacter woesei DSM 14684 NC_013739 1 0 forest soil isolated from forest soil and will be used for comparative analysis soil 158046 Coprococcus catus GD/7 NC_021009 1 0 human feces Clinical/Human-associated 152499 Coprococcus sp. ART55/1 NC_021018 1 0 human feces Clinical/Human-associated 72829 Coprothermobacter proteolyticus DSM 5265 NC_011295 1 0 tannery waste containing cattle manure Polluted/impacted environment 2911 Coraliomargarita akajimensis DSM 45221 NC_014008 1 0 Seawater surrounding the hard coral x Galaxea fascicularis; Majanohama, Akajima, Japan Aquatic-environment 216867 Corallococcus coralloides DSM 2259 NC_017030.1 1 0 soil; obtained from the DSMZ (Deutsche Sammlung von Mikrooganismen und Zellkulturen GmbH soil 157054 Coriobacterium glomerans PW2 NC_015389 1 0 midgut of Pyrrhocoris apterus L. (red soldier bug) Insect-associated/other symbiont 288793 Corynebacterium argentoratense DSM 44202 NC_022198.1 1 0 throat culture Clinical/Human-associated 68407 Corynebacterium aurimucosum ATCC 700975 NC_012590,NC_010813 1 1 the human female urogenital tract isolated from the human female urogenital tract and will be used for comparative analysis Clinical/Human-associated 278465 Corynebacterium callunae DSM 20147 NC_020506.1,NC_020523.1,NC_020553.1 1 2 heather isolated from heather, Mineral and Chem. Corp Plant/agriculture-associated 150904 Corynebacterium diphtheriae 241 NC_016782 1 0 diphtheria patient Clinical/Human-associated 157788 Corynebacterium diphtheriae 31A NC_016799 1 0 diphtheria patient (vaccinated adult) Clinical/Human-associated 155681 Corynebacterium diphtheriae BH8 NC_016800 1 0 patient in Rio de Janeiro Clinical/Human-associated 157008 Corynebacterium diphtheriae C7 (beta) NC_016801 1 0 Derivative of the a virulent isolate C7, 1954 Lab/Engineered 147831 Corynebacterium diphtheriae CDCE 8392 NC_016785 1 0 diptheria patient Clinical/Human-associated 148788 Corynebacterium diphtheriae HC01 NC_016786 1 0 blood sample from a patient with fatal endocarditis Clinical/Human-associated 150027 Corynebacterium diphtheriae HC02 NC_016802 1 0 blood sample from a patient with endocarditis Clinical/Human-associated 151188 Corynebacterium diphtheriae HC03 NC_016787 1 0 blood sample from a patient with endocarditis Clinical/Human-associated 148977 Corynebacterium diphtheriae HC04 NC_016788 1 0 blood sample from a patient with fatal endocarditis Clinical/Human-associated 158328 Corynebacterium diphtheriae INCA 402 NC_016783 1 0 blood sample from a patient with fatal endocarditis Clinical/Human-associated 47633 Corynebacterium diphtheriae NCTC 13129 NC_002935 1 0 the pharyngeal membrane of a 72-year-old unimmunized UK female with Clinical/Human-associated diphtheria acquired during a short Baltic cruise isolated in 1997 from the pharyngeal membrane of a 72-year-old unimmunized UK female with Clinical/Human-associated diphtheria acquired during a short Baltic cruise Clinical/Human-associated 148536 Corynebacterium diphtheriae PW8 NC_016789 1 0 diphtheria patient in New York, 1896 Clinical/Human-associated 157681 Corynebacterium diphtheriae VA01 NC_016790 1 0 diphtheria patient Clinical/Human-associated 9312 Corynebacterium efficiens YS-314 NC_004369,NC_004320,NC_004319 1 2 soils at Kanagawa, Japan isolated by researchers of Ajinomoto food company from soils at Kanagawa, Japan in the late 1980's soil 77853 Corynebacterium glutamicum ATCC 13032 NC_006958 1 0 isolated in the late 1950's Clinical/Human-associated 203724 Corynebacterium glutamicum ATCC 13032 NC_003450 1 0 isolated in the late 1950's Clinical/Human-associated Corynebacterium glutamicum K051 NC_020519 1 0 mutant strain Lab/engineered 280145 Corynebacterium glutamicum MB001 NC_022040.1 1 0 soil soil 58097 Corynebacterium glutamicum R NC_009342,NC_009343 1 1 meadow soil isolated from meadow soil in Japan and will be used for comparative analysis soil 297567 Corynebacterium glutamicum SCgG1 NC_021351.1 1 0 soil soil 296520 Corynebacterium glutamicum SCgG2 NC_021352.1 1 0 soil soil 246244 Corynebacterium halotolerans YIM 70093 = DSM 44683 NC_020302.1,NC_020303.1 1 1 saline soil saline soil Extreme-environment 31838 Corynebacterium jeikeium K411 NC_007164,NC_003080 1 1 the axilla of a bone marrow transplant patient isolated from the axilla of a bone marrow transplant patient Clinical/Human-associated 120627 Corynebacterium kroppenstedtii DSM 44385 NC_012704 1 0 human sputum isolated from human sputum Clinical/Human-associated 256873 Corynebacterium maris DSM 45190 NC_021915.1,NC_021920.1 1 1 coral mucus isolated from coral mucus Aquatic-life-associated 214597 Corynebacterium pseudotuberculosis 1/06-A NC_017308 1 0 Isolated from a Horse in North America. equine field isolate Terrestrial-animal-associated 156913 Corynebacterium pseudotuberculosis 1002 NC_017300 1 0 goat caseous granulomas came from the microorganism collection of the Institute of Health Sciences of the Federal University of Bahia and was isolated from goat caseous granulomas found in Bahia state, confirmed by biochemical tests (API CORYNE, Bio-Merieux SA, France) Terrestrial-animal-associated 234767 Corynebacterium pseudotuberculosis 258 NC_017945.1 1 0 horse with ulcerative lymphangitis Terrestrial-animal-associated 233410 Corynebacterium pseudotuberculosis 267 NC_017462.1 1 0 abscess from caseous lymphadenitis from llama Terrestrial-animal-associated 217026 Corynebacterium pseudotuberculosis 3/99-5 NC_016781 1 0 case of naturally-occurring Caseous Lymphadenitis (CLA) isolate from a case of naturally-occurring Caseous Lymphadenitis (CLA) in a sheep in the Scottish Borders in 1999 Terrestrial-animal-associated 230388 Corynebacterium pseudotuberculosis 31 NC_017730.1 1 0 From a large brisket swelling of a buffalo Terrestrial-animal-associated 235359 Corynebacterium pseudotuberculosis 316 NC_016932.1 1 0 Horse abscess Terrestrial-animal-associated 206259 Corynebacterium pseudotuberculosis 42/02-A NC_017306 1 0 Isolated from natural outbreaks of caseous lymphadenitis in Perth, Australia. Terrestrial-animal-associated 140234 Corynebacterium pseudotuberculosis C231 NC_017301 1 0 Isolated from an ovine host in Australia. Terrestrial-animal-associated 181970 Corynebacterium pseudotuberculosis CIP 52.97 NC_017307 1 0 lymphangitis from a horse Isolated in 1952 from a case of ulcerative lymphangitis in a Kenyan horse. Terrestrial-animal-associated 234602 Corynebacterium pseudotuberculosis Cp162 NC_018019.1 1 0 caseous lymphadenitis neck abscess Terrestrial-animal-associated 165161 Corynebacterium pseudotuberculosis FRC41 NC_014329 1 0 inguinal lymph node of a 12-year-old girl with necrotizing lymphadenitis Clinical/Human-associated 169742 Corynebacterium pseudotuberculosis I19 NC_017303 1 0 abscess of mastitis from a bovine Isolated from a dairy cow in Israel with severe clinical mastitis. Terrestrial-animal-associated 233098 Corynebacterium pseudotuberculosis P54B96 NC_017031.1 1 0 liver, lung, mediastinal lymph node lesions of antelope Terrestrial-animal-associated 182071 Corynebacterium pseudotuberculosis PAT10 NC_017305 1 0 Collected from a lung abscess in an Argentine sheep in Patagonia. isolated from the abscess of lung from a sheep Terrestrial-animal-associated 248099 Corynebacterium terpenotabidum Y-11 NC_021663.1 1 0 soil soil 188041 Corynebacterium ulcerans 0102 NC_018101 1 0 Obtained in 2001 from the pharyngeal pseudomembrane of a 52-year-old woman presenting with a sore throat and fever in Japan. human Clinical/Human-associated isolate Clinical/Human-associated 179178 Corynebacterium ulcerans 809 NC_017317 1 0 isolated from an elderly woman with fatal pulmonary infection Clinical/Human-associated 175797 Corynebacterium ulcerans BR-AD22 NC_015683 1 0 Obtained from a nasal sample of a 5-year-old female dog kept in an animal shelter in the metropolitan area of Rio de Janeiro. a nasal sample of an asymptomatic dog Terrestrial-animal-associated 58120 Corynebacterium urealyticum DSM 7109 NC_010545 1 0 case of cystitis isolated from a case of cystitis Clinical/Human-associated 267917 Corynebacterium urealyticum DSM 7111 NC_020230.1 1 0 ectopic kidney of a 9-year-old patient isolated from a 9-year-old male with ectopic kidney Clinical/Human-associated 10955 Coxiella burnetii CbuG_Q212 NC_011527 1 0 case of endocarditis and does not carry a plasmid isolated from a case of endocarditis and does not carry a plasmid Clinical/Human-associated 77120 Coxiella burnetii CbuK_Q154 NC_011528,NC_011526 1 1 patient with endocarditis and contains the plasmid QpRS isolated from a patient with endocarditis and contains the plasmid QpRS Clinical/Human-associated 32972 Coxiella burnetii Dugway 5J108-111 NC_009727,NC_009726 1 1 Blood Blood Terrestrial-animal-associated 33747 Coxiella burnetii RSA 331 NC_010117,NC_010115 1 1 the blood of an infected patient isolated from the blood of an infected patient in northern Italy in 1945 Clinical/Human-associated 82552 Coxiella burnetii RSA 493 NC_002971,NC_004704 1 1 This is a Nine Mile phase I isolate Clinical/Human-associated 239080 Crinalium epipsammum PCC 9333 NC_019753.1,NC_019737.1,NC_019755.1,NC_019733.1,NC_019756.1,NC_019736.1,NC_019735.1,NC_019754.1,NC_019734.1 1 8 phtosysthesis related unknown 46233 Croceibacter atlanticus HTCC2559 NC_014230 1 0 Sargasso Sea at a depth of 10 meters isolated from the Sargasso Sea at a depth of 10 meters Aquatic-environment 107175 Cronobacter sakazakii ATCC BAA-894 NC_009778,NC_009780,NC_009779 1 2 isolated from powdered baby milk formula associated with a NICU outbreak Food-associated 322076 Cronobacter sakazakii CMCC 45402 NC_023032.1,NC_023025.1,NC_023024.1 1 2 milk Food-associated 234768 Cronobacter sakazakii ES15 NC_017933.1 1 0 ground whole grains Food-associated 185200 Cronobacter sakazakii SP291 NC_020260.1,NC_020263.1,NC_020261.1,NC_020262.1 1 3 isolate cultured from a powdered infant formula production facility. Production-site-facility 150968 Cronobacter turicensis z3032 NC_013282,NC_013285,NC_013284,NC_013283 1 3 human neonatal meningitis, blood culture Clinical/Human-associated 116861 Cryptobacterium curtum DSM 15641 NC_013170 1 0 periodontal pocket of an adult human with periodontal disease isolated in 1995 from a periodontal pocket of an adult human with periodontal disease Clinical/Human-associated 4734 Cupriavidus metallidurans CH34 NC_007973,NC_007974,NC_007971,NC_007972 1 3 sedimentation pond in a zinc factory, Belgium Polluted/impacted environment 201015 Cupriavidus necator N-1 NC_015726,NC_015727,NC_015723,NC_015724 2 2 soil, University Park, PA soil 42494 Cupriavidus taiwanensis NC_010528,NC_010530,NC_010529 2 1 the root nodule of the legume Mimosa pudica isolated from the root nodule of the legume Mimosa pudica in Taiwan and will be used for comparative genomics Plant/agriculture-associated 239906 Cyanobacterium aponinum PCC 10605 NC_019776.1,NC_019777.1 1 1 fresh water Aquatic-environment 112915 Cyanobacterium stanieri PCC 7202 NC_019778.1 1 0 alkaline pod isolated by M Lefevre in 1963 Extreme-environment 151080 cyanobacterium UCYN-A NC_013771 1 0 Candidatus Atelocyanobacterium thalassa isolate ALOHA isolated from an intertidal habitat Aquatic-environment 100512 Cyanobium gracile PCC 6307 NC_019675.1 1 0 lake water Aquatic-environment 130209 Cyanothece sp. ATCC 51142 NC_010546,NC_010542,NC_010543,NC_010539,NC_010547,NC_010541 2 4 intertidal sands from the Gulf of Mexico isolated from intertidal sands from the Gulf of Mexico in Texas Aquatic-environment 136448 Cyanothece sp. PCC 7424 NC_011729,NC_011737,NC_011730,NC_011732,NC_011733,NC_011734,NC_011738 1 6 rice field isolated from a rice field in Senegal Plant/agriculture-associated 30657 Cyanothece sp. PCC 7425 NC_011884,NC_011885,NC_011882,NC_011880 1 3 rice field isolated from a rice field in Senegal Plant/agriculture-associated 18455 Cyanothece sp. PCC 7822 NC_014501,NC_014504,NC_014503,NC_014502,NC_014535,NC_014534,NC_014533 1 6 rice fields isolated from rice fields in Cuttack, Orissa, India Plant/agriculture-associated 125535 Cyanothece sp. PCC 8801 NC_011726,NC_011723,NC_011727,NC_011721 1 3 rice fields isolated from rice fields in Taiwan Plant/agriculture-associated 112625 Cyanothece sp. PCC 8802 NC_013161,NC_013160,NC_013167,NC_013168,NC_013163 1 4 rice fields isolated from rice fields in southern Taiwan Plant/agriculture-associated 172075 Cyclobacterium marinum DSM 745 NC_015914 1 0 Coelomic fluid of a sand dollar (Poronotus triacanthus) Aquatic-life-associated 131878 Cycloclasticus sp. P1 NC_018697.1 1 0 Deep-sea sediments of the Pacific Ocean Aquatic-environment 247860 Cycloclasticus zancles 7-ME NC_021917.1,NC_021918.1 1 1 tar at the shipwreck site of tanker Haven Polluted/impacted environment 108647 Cylindrospermum stagnale PCC 7417 NC_019757.1,NC_019758.1,NC_020050.1,NC_019744.1 1 3 Soil, greenhouse Plant/agriculture-associated 34013 Cytophaga hutchinsonii ATCC 33406 NC_008255 1 0 seawater Aquatic-environment 132842 Dactylococcopsis salina PCC 8305 NC_019780.1 1 0 solar lake Extreme-environment 89105 Dechloromonas aromatica RCB NC_007298 1 0 Potomac River Maryland Aquatic-environment 130492 Dechlorosoma suillum PS NC_016616 1 0 animal waste lagoons Polluted/impacted environment 107323 Deferribacter desulfuricans SSM1 NC_013939,NC_013940 1 1 deep-sea hydrothermal vent chimney at the Suiyo Seamount isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan Extreme-environment 228777 Dehalobacter sp. CF NC_018867.1 1 0 enrichment culture derived from an enrichment culture (anaerobic mixed microbial cultures capable of reductive dechlorination of chlorinated ethanes and chloroform) Polluted/impacted environment 237672 Dehalobacter sp. DCA NC_018866.1 1 0 1,1,1-trichloroethane dechlorinating enrichment derived from a 1,1,1-trichloroethane dechlorinating enrichment Polluted/impacted environment 89364 Dehalococcoides ethenogenes 195 NC_002936 1 0 anaerobic sewage digestor. Polluted/impacted environment 241727 Dehalococcoides mccartyi BTF08 NC_020387.1 1 0 isolated in Bitterfeld Plant/agriculture-associated 245899 Dehalococcoides mccartyi DCMB5 NC_020386.1 1 0 the contaminated Spittelwasser creek near Bitterfeld isolated from the contaminated Spittelwasser creek near Bitterfeld Polluted/impacted environment 311560 Dehalococcoides mccartyi GY50 NC_022964.1 1 0 plant growth promoting unknown 128035 Dehalococcoides sp. BAV1 NC_009455 1 0 chloroethene-contaminated Bachman Road site in Oscoda Polluted/impacted environment 125902 Dehalococcoides sp. CBDB1 NC_007356 1 0 enriched chlorobenzene-dechlorinatng mixed culture from anoxic river sediment isolated from an enriched chlorobenzene-dechlorinatng mixed culture from anoxic river sediment Polluted/impacted environment 13473 Dehalococcoides sp. GT NC_013890 1 0 chloroethene-contaminated aquifer isolated from an chloroethene-contaminated aquifer Polluted/impacted environment 95780 Dehalococcoides sp. VS NC_013552 1 0 Polluted/impacted environment 78720 Dehalogenimonas lykanthroporepellens BL-DC-9 NC_014314 1 0 Waste recovery well at the Petro-Processors of Louisiana, Inc. Superfund Site Polluted/impacted environment 121019 Deinococcus deserti VCD115 NC_012526,NC_012527,NC_012529,NC_012528 1 3 gamma-irradiated Sahara desert sand isolated from gamma-irradiated Sahara desert sand Extreme-environment 41128 Deinococcus geothermalis DSM 11300 NC_008025,NC_009939,NC_008010 1 2 hot spring at Agnano, Naples, Italy isolated from a hot spring at Agnano, Naples, Italy and will be used for comparative analysis with other radiation resistant bacteria Extreme-environment 152785 Deinococcus gobiensis I-0 NC_017790.1,NC_017791.1,NC_017792.1,NC_017793.1,NC_017806.1,NC_017805.1,NC_017771.1 1 6 Sand sample of the Gobi desert inxinjiang Autonomous Region, China soil 159729 Deinococcus maricopensis DSM 21211 NC_014958 1 0 Sonoran desert soil soil 179204 Deinococcus peraridilitoris DSM 19664 NC_019793.1,NC_019789.1,NC_019790.1 1 2 Arid soil collected from a coastal desert north of Antofagasta in Chile soil 159979 Deinococcus proteolyticus MRP NC_015161,NC_015162,NC_015163,NC_015169,NC_015170 1 4 Faeces of Lama glama Terrestrial-animal-associated 64572 Deinococcus radiodurans R1 NC_001263,NC_001264,NC_000958,NC_000959 2 2 uv resistant unknown 41351 Delftia acidovorans SPH-1 NC_010002 1 0 Sludge from communal sewage treatment plant; Germany Polluted/impacted environment 157857 Delftia sp. Cs1-4 NC_015563 1 0 PAH contaminated soils in Wisconsin Polluted/impacted environment 54242 Denitrovibrio acetiphilus DSM 12809 NC_013943 1 0 Oil reservoir model column Extreme-environment 100999 Desulfarculus baarsii DSM 2075 NC_014365 1 0 Ditch mud; Germany Aquatic-environment 8144 Desulfatibacillum alkenivorans AK-01 NC_011768 1 0 sediment from the Arthur Kill, NJ/NY waterway isolated from sediment from the Arthur Kill, NJ/NY waterway Aquatic-environment 15223 Desulfitobacterium hafniense DCB-2 NC_011830 1 0 municipal sludge isolated from municipal sludge Polluted/impacted environment 65307 Desulfitobacterium hafniense Y51 NC_007907 1 0 soil contaminated with tetrachloroethene (PCE) isolated from soil contaminated with tetrachloroethene (PCE) in Japan Polluted/impacted environment 170587 Desulfobacca acetoxidans DSM 11109 NC_015388 1 0 Anaerobic granular sludge of a pilot-scale UASB reactor (1.7 1) fed with acetate and an excess of sulfate. Polluted/impacted environment 25181 Desulfobacterium autotrophicum HRM2 NC_012108,NC_012109 1 1 marine sediment isolated from a marine sediment in the Mediterranean sea near Venice, Italy Aquatic-environment 47847 Desulfobacula toluolica Tol2 NC_018645.1 1 0 Isolated from a sulfide-rich marine sediment. Marine mud; USA Extreme-environment 114934 Desulfobulbus propionicus DSM 2032 NC_014972 1 0 anaerobic mud in Germany Extreme-environment 232581 Desulfocapsa sulfexigens DSM 10523 NC_020304.1,NC_020305.1 1 1 Mud flat in Arcachon, France Aquatic-environment 35880 Desulfococcus oleovorans Hxd3 NC_009943 1 0 oil/water mixture from an oil production plant isolated from an oil/water mixture from an oil production plant Polluted/impacted environment 71890 Desulfohalobium retbaense DSM 5692 NC_013223,NC_013224 1 1 the hypersaline Lake Retba isolated from the hypersaline Lake Retba in Senegal, Africa and will be used for comparative analysis Extreme-environment 69216 Desulfomicrobium baculatum DSM 4028 NC_013173 1 0 manganese ore isolated from manganese ore and is able to reduce sulfate to sulfide Extreme-environment 156970 Desulfomonile tiedjei DSM 6799 NC_018025.1,NC_018026.1 1 1 sewage sludge Polluted/impacted environment 162091 Desulfosporosinus orientis DSM 765 NC_016584 1 0 Soil at pumping station near rising main Rangoon Road soil 67261 Desulfotalea psychrophila LSv54 NC_006138,NC_006139,NC_006140 1 2 marine sediments off of the coast of Svalbard, and can grow at temperatures as low as -1 isolated from marine sediments off of the coast of Svalbard, and can grow at temperatures as low as -1 Aquatic-environment 42372 Desulfotomaculum acetoxidans DSM 771 NC_013216 1 0 pig waste isolated from pig waste Polluted/impacted environment 168000 Desulfotomaculum carboxydivorans CO-1-SRB NC_015565 1 0 Sludge from an anaerobic bioreactor treating paper mill wastewater Polluted/impacted environment 162030 Desulfotomaculum kuznetsovii DSM 6115 NC_015573 1 0 underground thermal mineral water Extreme-environment 82656 Desulfotomaculum reducens MI-1 NC_009253 1 0 heavy metal-contaminated sediment collected at the Mare Island Naval Shipyard on the San Francisco Bay isolated from heavy metal-contaminated sediment collected at the Mare Island Naval Shipyard on the San Francisco Bay Polluted/impacted environment 155601 Desulfotomaculum ruminis DSM 2154 NC_015589 1 0 rumen of hay-fed sheep Terrestrial-animal-associated 51796 Desulfovibrio aespoeensis Aspo-2 NC_014844 1 0 Granitic rock aquifer at 600 m depth; Sweden, Dspv Island Aquatic-environment 50650 Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 NC_011883 1 0 the rumen of a sheep isolated from the rumen of a sheep and will be used for comparative analysis with other sulfate-reducing bacteria Terrestrial-animal-associated 50040 Desulfovibrio desulfuricans subsp. desulfuricans str. G20 NC_007519 1 0 oil well corrosion site isolated from an oil well corrosion site Polluted/impacted environment 274292 Desulfovibrio hydrothermalis AM13 = DSM 14728 NC_020055.1,NC_019953.1 1 1 deep-sea hydrothermal chimney sample isolated from a deep-sea hydrothermal chimney sample collected at 13????? N on the East-Pacific Rise at a depth of 2600 m. D. hydrothermalis is piezophilic, having an optimal growth at 25 MPa Extreme-environment 26496 Desulfovibrio magneticus RS-1 NC_012796,NC_012797,NC_012795 1 2 freshwater sulphide-rich mud from a waterway near Kamena River, Wakayama prefecture, Japan Polluted/impacted environment 170198 Desulfovibrio piezophilus NC_020409.1 1 0 deep-sea wood falls deep-sea wood falls Aquatic-environment 121003 Desulfovibrio salexigens DSM 2638 NC_012881 1 0 mud in British Guyana Aquatic-environment 62463 Desulfovibrio vulgaris DP4 NC_008751,NC_008741 1 1 heavy metal-Impacted environment lake sediment Polluted/impacted environment Desulfovibrio vulgaris RCH1 NC_017310,NC_017311 1 1 chromium‐contaminated  groundwater Polluted/impacted environment 119526 Desulfovibrio vulgaris str. Hildenborough NC_002937,NC_005863 1 1 clay soil near Hildenborough, UK isolated from clay soil near Hildenborough, UK in 1946 soil 86729 Desulfovibrio vulgaris str. 'Miyazaki F' NC_011769 1 0 unknown 86994 Desulfurispirillum indicum S5 NC_014836 1 0 River sediment; India, Chennai, Buckingham Canal, Chepauk Aquatic-environment 70802 Desulfurivibrio alkaliphilus AHT2 NC_014216 1 0 Sediments from a highly alkaline saline soda lake in Egypt Extreme-environment 167085 Desulfurobacterium thermolithotrophum DSM 11699 NC_015185 1 0 Deep-sea hydrothermal vent chimney; Mid-Atlantic Ridge Extreme-environment 48475 Dichelobacter nodosus VCS1703A NC_009446 1 0 Terrestrial-animal-associated 25310 Dickeya dadantii 3937 NC_014500 1 0 Saintpaulia plants isolated from Saintpaulia plants Plant/agriculture-associated 110536 Dickeya dadantii Ech586 NC_013592 1 0 Plant/agriculture-associated 95084 Dickeya dadantii Ech703 NC_012880 1 0 Plant/agriculture-associated 111179 Dickeya zeae Ech1591 NC_012912 1 0 Plant/agriculture-associated 33784 Dictyoglomus thermophilum H-6-12 NC_011297 1 0 Slightly alkaline Tsuetae Hot spring in Kumamoto Prefecture in Japan Extreme-environment 93964 Dictyoglomus turgidum DSM 6724 NC_011661 1 0 Hot spring, Uzon volcano caldera; USSR, Kamchatka Extreme-environment 9476 Dinoroseobacter shibae DFL 12 NC_009952,NC_009956,NC_009957,NC_009958,NC_009959,NC_009955 1 5 Marine dinoflagellates from the Bay of Tokyo Aquatic-life-associated 416 Dyadobacter fermentans DSM 18053 NC_013037 1 0 surface sterilized stems of Zea mays, however, tests to determine whether this organism grows as an endophyte were inconclusive isolated from surface sterilized stems of Zea mays, however, tests to determine whether this organism grows as an endophyte were inconclusive Plant/agriculture-associated 187570 Echinicola vietnamensis DSM 17526 NC_019904.1 1 0 seawater from mussel farm Seawater collected in a musselfarm; Vietnam, South China Sea, Nha Trang Bay Aquatic-environment 114273 Edwardsiella ictaluri 93-146 NC_012779 1 0 Enteric septicemia of catfish outbreak in a commercial catfish pond in Louisiana Aquatic-life-associated 266281 Edwardsiella tarda C07-087 NC_020796.1 1 0 large outbreaks of gastrointestinal septicemia isolated from large outbreaks of gastrointestinal septicemia in commercial catfish operations Aquatic-life-associated 116525 Edwardsiella tarda EIB202 NC_013508,NC_013509 1 1 diseased turbot (Scophthalmus maximus) in a mariculture farm in Yantai, Shandong province of China Aquatic-life-associated 147555 Edwardsiella tarda FL6-60 NC_017309,NC_017318 1 1 cases of septicemia and meningitis, primarily in immunocompromised patients Clinical/Human-associated 106823 Eggerthella lenta DSM 2243 NC_013204 1 0 cases of bacteremia isolated from cases of bacteremia, isolated from a rectal tumor in 1935 Clinical/Human-associated 72831 Eggerthella sp. YY7918 NC_015738 1 0 solated from adult human intestine Clinical/Human-associated 118076 Ehrlichia canis str. Jake NC_007354 1 0 2-year-old male dog isolated in 1989 in North Carolina from a 2-year-old male dog Terrestrial-animal-associated 103583 Ehrlichia chaffeensis str. Arkansas NC_007799 1 0 patient obtained from a patient on an army base in Arkansas in 1990 Clinical/Human-associated 325700 Ehrlichia muris AS145 NC_023063.1 1 0 spleen of wild mouse isolated from a wild mouse in 1983 in Japan Terrestrial-animal-associated 72196 Ehrlichia ruminantium str. Gardel NC_006831 1 0 the Caribbean island of Guadeloupe isolated from the Caribbean island of Guadeloupe and will be used for comparative genomics Terrestrial-animal-associated 92411 Ehrlichia ruminantium str. Welgevonden NC_006832 1 0 nfected tick obtained from an infected tick and maintained by serial infection in mice Terrestrial-animal-associated 203725 Ehrlichia ruminantium str. Welgevonden NC_005295 1 0 infected tick isolated in mice from an infected tick Insect-associated/other symbiont 86178 Elusimicrobium minutum Pei191 NC_010644 1 0 Pachnoda ephippiata Insect-associated/other symbiont 181523 Emticicia oligotrophica DSM 17448 NC_018748,NC_018742,NC_018749,NC_018743,NC_018744,NC_018745 1 5 warm spring water Extreme-environment 178747 Enterobacter aerogenes EA1509E NC_020181,NC_020180,NC_020182 1 2 blood culture isolate from blood culture Clinical/Human-associated 192003 Enterobacter aerogenes KCTC 2190 NC_015663 1 0 sputum, South Carolina Dept. of Health and Environmental Control Clinical/Human-associated 216248 Enterobacter asburiae LF7a NC_015968,NC_015963,NC_015969 1 2 unknown 204430 Enterobacter cloacae EcWSU1 NC_016514,NC_016515 1 1 onion bulbs Plant/agriculture-associated 171306 Enterobacter cloacae SCF1 NC_014618 1 0 Short Cloud Forest soil soil Enterobacter cloacae subsp. cloacae ATCC 13047 NC_014121,NC_014107,NC_014108 1 2 Isolated from human cerebrospinal fluid by Edwin Oakes Jordan in 1890. Clinical/Human-associated 247268 Enterobacter cloacae subsp. cloacae ENHKU01 NC_018405.1 1 0 isolated from a diseased pepper (Capsicum annuum) plant in Hong Kong Plant/agriculture-associated 152217 Enterobacter cloacae subsp. cloacae NCTC 9394 NC_021046 1 0 Human faeces, Montevideo, Uruguay in 1955 Clinical/Human-associated Enterobacter cloacae subsp. dissolvens SDM NC_018079 1 0 Isolated from orchard soil samples in Jinan, China. soil 101211 Enterobacter sp. 638 NC_009436,NC_009425 1 1 Populus trichocarpa x deltoides Plant/agriculture-associated 234870 Enterobacter sp. R4-368 NC_021500.1,NC_021492.1 1 1 Jatropha surface sterilized roots Plant/agriculture-associated Enterobacteriaceae bacterium FGI 57 NC_020063 1 0 Isolated in 2009 from a fungus garden of the leaf-cutter ant Atta colombica on Pipeline Road in Panama Insect-associated/other symbiont Enterococcus casseliflavus EC20 NC_020995 1 0 Antibiotic resistant clinical isolate Clinical/Human-associated 176554 Enterococcus faecalis 62 NC_017312,NC_017314,NC_017313,NC_017315 1 3 healthy Norwegian baby isolate from a healthy Norwegian baby in 2006 Clinical/Human-associated 246736 Enterococcus faecalis D32 NC_018221.1,NC_018222.1,NC_018223.1 1 2 pig feces isolated from pig feces in 2001 in Denmark Terrestrial-animal-associated Enterococcus faecalis OG1R NC_017316 1 0 OG1RF is a rifampicin and fusidic acid resistant derivative of OG1 Clinical/Human-associated 265187 Enterococcus faecalis str. Symbioflor 1 NC_019770.1 1 0 Stool specimen of healthy human adult Clinical/Human-associated 7065 Enterococcus faecalis V583 NC_004668,NC_004669,NC_004671,NC_004670 1 3 blood culture derived from a chronically-infected patient came from a blood culture derived from a chronically-infected patient in 1987 from Barnes Hospital in St Clinical/Human-associated 233823 Enterococcus faecium Aus0004 NC_017022,NC_017032,NC_017023,NC_017024 1 3 the bloodstream of a patient isolated from the bloodstream of a patient in Melbourne, Australia in 1998 Clinical/Human-associated 280489 Enterococcus faecium Aus0085 NC_021994.1,NC_021995.1,NC_021989.1,NC_021987.1,NC_021996.1,NC_021988.1,NC_021990.1 1 6 the bloodstream of a patient isolated Aus0085, isolated from the bloodstream of a patient in Melbourne, Australia in 2009 Clinical/Human-associated Enterococcus faecium DO NC_017960,NC_017961,NC_017962,NC_017963 1 3 Isolated from the blood of a patient with endocarditis. Clinical/Human-associated 230477 Enterococcus faecium NRRL B-2354 NC_020207.1,NC_020208.1 1 1 milk and dairy utensils cheese Food-associated 163807 Enterococcus hirae ATCC 9790 NC_018081.1,NC_015845.1 1 1 Lab/Engineered 281267 Enterococcus mundtii QU 25 NC_022878.1,NC_022879.1,NC_022884.1,NC_022880.1,NC_022881.1,NC_022883.1 1 5 isolated from ovine faeces Terrestrial-animal-associated 14464 Enterococcus sp. 7L76 NC_021023 1 0 human intestine cellulolytic bacterium from the human intestine Clinical/Human-associated 154257 Erwinia amylovora ATCC 49946 NC_013972,NC_013973,NC_013971 1 2 Plant-derived foodstuff (Apple, Malus pumila cv. Rhode Island Greening) Plant/agriculture-associated Erwinia amylovora ATCC 49946 NC_013971,NC_013972,NC_013973 1 2 Causative agent of fire blight that affects rosaceous plants, especially pear and apple. Plant/agriculture-associated 142366 Erwinia amylovora CFBP1430 NC_013957,NC_013961 1 1 Crataegus sp. Plant/agriculture-associated Erwinia amylovora CFBP1430 NC_013961,NC_013957 1 1 Causative agent of fire blight that affects rosaceous plants, especially pear and apple. Plant/agriculture-associated Erwinia billingiae Eb661 NC_014306,NC_014305,NC_014304 1 2 Plant/agriculture-associated 40668 Erwinia pyrifoliae DSM 12163 NC_017390,NC_017392,NC_017389,NC_017388,NC_017391 1 4 Necrotic tissue of Pyrus pyrifolia; South Korea Plant/agriculture-associated 67807 Erwinia pyrifoliae Ep1/96 NC_012214,NC_013265,NC_013264,NC_013263,NC_013954 1 5 Necrotic tissue of Pyrus pyrifolia; South Korea Plant/agriculture-associated 41759 Erwinia sp. Ejp617 NC_017445,NC_017442,NC_017446,NC_017443,NC_017447,NC_017444 1 5 Nashi pear Plant/agriculture-associated 9546 Erwinia tasmaniensis Et1/99 NC_010694,NC_010695,NC_010696,NC_010697,NC_010699,NC_010693 1 5 apple flowers isolated from apple flowers in Tasmania, Australia Plant/agriculture-associated 102657 Erythrobacter litoralis HTCC2594 NC_007722 1 0 Sargasso Sea at a depth of 10 meters collected from the Sargasso Sea at a depth of 10 meters Aquatic-environment 52250 Escherichia coli 042 NC_017626,NC_017627 1 1 Isolated from a child with diarrhea in the course of an epidemiologic study in Lima, Peru, in 1983. Clinical/Human-associated 77757 Escherichia coli 536 NC_008253 1 0 patient with acute pyelonephritis (inflammation of the kidney and pelvis) isolated from a patient with acute pyelonephritis (inflammation of the kidney and pelvis) Clinical/Human-associated 113220 Escherichia coli 55989 NC_011748 1 0 Clinical/Human-associated enteroaggregative isolate Clinical/Human-associated 35126 Escherichia coli ABU 83972 NC_017631,NC_017629 1 1 young female with long term asymptomatic bacteriuria (ABU) Clinical/Human-associated 127180 Escherichia coli APEC O1 NC_008563,NC_009838,NC_009837 1 2 Terrestrial-animal-associated 269726 Escherichia coli APEC O78 NC_020163.1 1 0 the lung of a turkey clinically diagnosed with colibacillosis isolated from the lung of a turkey clinically diagnosed with colibacillosis Terrestrial-animal-associated 82905 Escherichia coli ATCC 8739 NC_010468 1 0 human feces Clinical/Human-associated 118196 Escherichia coli B str. REL606 NC_012967 1 0 Derivative of E. coli strain B Lab/Engineered 200998 Escherichia coli BL21(DE3) NC_012971.2 1 0 Derivative of E. coli strain B Lab/Engineered 200999 Escherichia coli BL21(DE3) NC_012892.2 1 0 strain B derived from strain B and is commonly used for protein expression and purification Lab/Engineered 165499 Escherichia coli 'BL21-Gold(DE3)pLysS AG' NC_012947 1 0 Derivative of E. coli strain B Lab/Engineered 60876 Escherichia coli BW2952 NC_012759 1 0 λ placMu50 was introduced into MC4100 to generate MC4100(MuLac) strain BW2952 Lab/Engineered 75197 Escherichia coli CFT073 NC_004431 1 0 isolated at the University of Maryland Hospital Clinical/Human-associated 36761 Escherichia coli DH1 NC_017625 1 0 Derived from Escherichia coli MM294 Lab/Engineered Escherichia coli DH1 NC_017638 1 0 obtained from the National BioResource Project at the National Institute of Genetics, Shizuoka, Japan Lab/engineered 31211 Escherichia coli E24377A NC_009801,NC_009787,NC_009788,NC_009789,NC_009790,NC_009791,NC_009786 1 6 obtained from Maj. Carl Brinkley at Walter Reed Army Institute of Research Clinical/Human-associated 8292 Escherichia coli ED1a NC_011745,NC_011754 1 1 Faeces of a healthy man in 2000 in France Clinical/Human-associated 136115 Escherichia coli ETEC H10407 NC_017633.1,NC_017724.1,NC_017722.1,NC_017723.1,NC_017721.1 1 4 adult with cholera-like symptoms in the course of an epidemiologic study in Dacca, Bangladesh, prior to 1973 Clinical/Human-associated 77814 Escherichia coli HS NC_009800 1 0 laboratory scientist at Walter Reed Army Institute of Research human commensal isolate, isolated from a laboratory scientist at Walter Reed Army Institute of Research in 1978 (Levine, 1978) Clinical/Human-associated 26572 Escherichia coli IAI1 NC_011741 1 0 isolated from the faeces of a young healthy military conscript in the 1980s in France Clinical/Human-associated 51957 Escherichia coli IAI39 NC_011750 1 0 isolated from the urine of a patient with pyelonephritis in the 1980s in France Clinical/Human-associated 148715 Escherichia coli IHE3034 NC_017628 1 0 neonatal meningitis-associated strain isolated in Finland in 1976 Clinical/Human-associated 303269 Escherichia coli JJ1886 NC_022648.1,NC_022651.1,NC_022661.1,NC_022650.1,NC_022649.1,NC_022662.1 1 5 Patient Clinical/Human-associated 13896 Escherichia coli KO11FL NC_016902,NC_016904,NC_016903 1 2 Lab/Engineered Escherichia coli KO11FL NC_017660,NC_017661 1 1 was engineered in 1990 to produce ethanol by chromosomal insertion Lab/engineered 74806 Escherichia coli LF82 NC_011993 1 0 patient with Crohn's disease isolated from a patient with Crohn's disease Clinical/Human-associated 293565 Escherichia coli LY180 NC_022364.1 1 0 the widely used KO11 strain derived from the widely used KO11 strain Lab/Engineered 190496 Escherichia coli NA114 NC_017644 1 0 urine of a 70 year old male patient of prostatitis from Pune Clinical/Human-associated 146794 Escherichia coli O103:H2 str. 12009 NC_013353,NC_013354 1 1 patient in Japan Clinical/Human-associated 235472 Escherichia coli O104:H4 str. 2009EL-2050 NC_018650,NC_018651,NC_018654,NC_018652 1 3 Isolated from a human patient from a 2009 outbreak of E coli in the Republic of Georgia Clinical/Human-associated 240135 Escherichia coli O104:H4 str. 2009EL-2071 NC_018661.1,NC_018663.1,NC_018662.1 1 2 Isolated from a human patient from a 2009 outbreak of E coli in the Republic of Georgia Clinical/Human-associated 234630 Escherichia coli O104:H4 str. 2011C-3493 NC_018658.1,NC_018666.1,NC_018659.1,NC_018660.1 1 3 Isolated from US citizen afflicted with HUS after travel to Germany during the 2011 E coli oubreak Clinical/Human-associated 143187 Escherichia coli O111:H- str. 11128 NC_013364,NC_013366,NC_013367,NC_013368,NC_013370,NC_013365 1 5 patient in Japan Clinical/Human-associated 90278 Escherichia coli O127:H6 str. E2348/69 NC_011601,NC_011603,NC_011602 1 2 outbreak isolated in Taunton, United Kingdom, in 1969 during an outbreak of infantile diarrhea Clinical/Human-associated 74651 Escherichia coli O157:H7 str. EC4115 NC_011353,NC_011351,NC_011350 1 2 Clinical/Human-associated 44059 Escherichia coli O157:H7 str. EDL933 NC_002655,NC_007414 1 1 isolated during an outbreak in 1982 Clinical/Human-associated 129985 Escherichia coli O157:H7 str. Sakai NC_002695,NC_002128,NC_002127 1 2 isolated in a 1997 outbreak in Sakai, Japan Clinical/Human-associated 9396 Escherichia coli O157:H7 str. TW14359 NC_013008,NC_013010 1 1 spinach isolated from spinach during the E. coli outbreak in 2006 and will be used for comparative analysis Clinical/Human-associated 24965 Escherichia coli O26:H11 str. 11368 NC_013361,NC_013363,NC_013369,NC_013362,NC_014543 1 4 Clinical/Human-associated 154499 Escherichia coli O55:H7 str. CB9615 NC_013941,NC_013942 1 1 infant with diarrhea isolated from an infant with diarrhea in Germany in 2003 and confirmed to belong to the same multilocus sequence type (ST11) as the O157:H7 clone Clinical/Human-associated 221597 Escherichia coli O55:H7 str. RM12579 NC_017656.1,NC_017658.1,NC_017653.1,NC_017657.1,NC_017655.1,NC_017654.1 1 5 1975 isolated in the US, a California isolate from 1975 Clinical/Human-associated 208710 Escherichia coli O7:K1 str. CE10 NC_017646,NC_017647,NC_017648,NC_017649,NC_017650 1 4 isolated from the CSF of a neonate with meningitis Clinical/Human-associated 181005 Escherichia coli O83:H1 str. NRG 857C NC_017634,NC_017659 1 1 Clinical/Human-associated 170845 Escherichia coli P12b NC_017663.1 1 0 unknown Escherichia coli PMV-1 NC_022370,NC_022371 1 1 clinical/human-associated 91599 Escherichia coli S88 NC_011742,NC_011747 1 1 case of neonatal meningitis isolated from a case of neonatal meningitis and will be used for comparative analysis Clinical/Human-associated 83070 Escherichia coli SE11 NC_011415,NC_011408,NC_011411,NC_011413,NC_011416,NC_011419,NC_011407 1 6 Clinical/Human-associated 158062 Escherichia coli SE15 NC_013654.1,NC_013655.1 1 1 Clinical/Human-associated 6161 Escherichia coli SMS-3-5 NC_010498,NC_010486,NC_010487,NC_010488,NC_010485 1 4 toxic-metal contaminated site, Shipyard Creek, Charleston, South Carolina isolated from a toxic-metal contaminated site, Shipyard Creek, Charleston, South Carolina Polluted/impacted environment 174193 Escherichia coli str. 'clone D i14' NC_017652 1 0 Family fecal sample Clinical/Human-associated 170746 Escherichia coli str. 'clone D i2' NC_017651 1 0 Family fecal sample Clinical/Human-associated 59506 Escherichia coli str. K-12 substr. DH10B NC_010473 1 0 DH10 (which was derived from MC1061 which derived from DH10 (which was derived from MC1061 which in turn was derived from M182) Lab/Engineered 224152 Escherichia coli str. K-12 substr. MDS42 NC_020518.1 1 0 unknown 129921 Escherichia coli str. K-12 substr. MG1655 NC_000913 1 0 derived from strain W1485, which was derived by Joshua Lederberg from the original K-12 isolate obtained from a patient in 1922 derived from strain W1485, which was derived by Joshua Lederberg from the original K-12 isolate obtained from a patient in 1922 Clinical/Human-associated 107702 Escherichia coli str. K-12 substr. W3110 NC_007779.1 1 0 unknown 167775 Escherichia coli UM146 NC_017632,NC_017630 1 1 isolated from Ileal Crohn's disease biopsy tissue Clinical/Human-associated 32010 Escherichia coli UMN026 NC_011751,NC_011749,NC_011739 1 2 isolated from a woman with uncomplicated acute cystitis in 1999 in the USA Clinical/Human-associated 205269 Escherichia coli UMNF18 NZ_AGTD01000001.1,NZ_AGTD01000005.1,NZ_AGTD01000006.1,NZ_AGTD01000003.1,NZ_AGTD01000004.1,NZ_AGTD01000002.1 1 5 lesion swab of diarrheal isolate isolated from a nursery farm in Iowa in 2006 Terrestrial-animal-associated 159162 Escherichia coli UMNK88 NC_017641,NC_017645,NC_017642,NC_017639,NC_017640,NC_017643 1 5 isolated in 2007 from a farm in Minnesota Terrestrial-animal-associated 42261 Escherichia coli UTI89 NC_007946,NC_007941 1 1 woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis isolated from a woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis in a murine urinary tract infection model Clinical/Human-associated 139032 Escherichia coli W NC_017635,NC_017637,NC_017636 1 2 E. coli W (ATCC 9637) was originally isolated from the soil of a cemetery near Rutgers University around 1943 by Selman A. Waksman, around the same time he and Alan Schatz discovered streptomycin (Eliora Ron, personal communication). Waksman coined the term 'antibiotic', and his discovery of streptomycin (and many other antibiotics) led to him being awarded the Nobel Prize in Physiology or Medicine in 1952. The strain was termed "Waksman's strain" or "W strain" because it showed the highest sensitivity to streptomycin compared to other isolated E. coli strains in Waksman's collection (Archer et al., 2011 PMID: 21208457) Soil Escherichia coli W NC_017664,NC_017665,NC_017662 1 2 soil near rutgers university soil 152722 Escherichia coli Xuzhou21 NC_017906.1,NC_017903.1,NC_017907.1 1 2 Clinical/Human-associated 122920 Escherichia fergusonii ATCC 35469 NC_011740,NC_011743 1 1 human feces isolated from human feces and will be used for comparative analysis with other Escherichia species Clinical/Human-associated 145175 Ethanoligenens harbinense YUAN-3 NC_014828 1 0 Anaerobic activated sludge of molasses wastewater in a continuous stirred-tank reactor Polluted/impacted environment 154092 Eubacterium cylindroides T2-87 NC_021019 1 0 Clinical/Human-associated 113401 Eubacterium eligens ATCC 27750 NC_012778,NC_012780,NC_012782 1 2 Human gut Clinical/Human-associated 172772 Eubacterium limosum KIST612 NC_014624 1 0 anaerobic digester and has a high growth rate on synthesis gas (CO; carbon monoxide) using it as a sole energy source isolated from an anaerobic digester and has a high growth rate on synthesis gas (CO; carbon monoxide) using it as a sole energy source Production-site-facility 107985 Eubacterium rectale ATCC 33656 NC_012781 1 0 human feces isolated from human feces Clinical/Human-associated 131464 Eubacterium rectale DSM 17629 NC_021010 1 0 Clinical/Human-associated 155814 Eubacterium rectale M104/1 NC_021044 1 0 Clinical/Human-associated 135646 Eubacterium siraeum NC_021011 1 0 Clinical/Human-associated 152769 Eubacterium siraeum V10Sc8a NC_021043 1 0 Clinical/Human-associated 238891 Exiguobacterium antarcticum B7 NC_018665.1 1 0 biofilm isolated from biofilm in Ginger lake localized in Antarctica will allow the investigation of genomic attributes that can be involved to adaptations of organisms under different thermal regimes which will help transcriptome and proteome studies to discover genes involved in metabolic pathways of adaptation to cold Extreme-environment 53410 Exiguobacterium sibiricum 255-15 NC_010556,NC_010550,NC_010549 1 2 2-3 million-year permafrost core isolated from a 2-3 million-year permafrost core in Siberia, Russia and can survive and grow rapidly at low temperatures Extreme-environment 39724 Exiguobacterium sp. AT1b NC_012673 1 0 Yellowstone National Park isolated from Yellowstone National Park and is a moderate thermophile Extreme-environment 310198 Exiguobacterium sp. MH3 NC_022794.1 1 0 rhizosphere of Lemna minor isolated from rhizosphere of Lemna minor sampled in China will allow the investigation of genomic attributes that can be involved to adaptations of organisms under a wide range of conditions which will help transcriptome and proteome studies to discover genes involved in metabolic pathways of adaptation, and also provide useful information related to interaction between Exiguobacterium spp Plant/agriculture-associated 148460 Faecalibacterium prausnitzii NC_021020 1 0 Clinical/Human-associated 154692 Faecalibacterium prausnitzii L2-6 NC_021042 1 0 Clinical/Human-associated 3052 Ferrimonas balearica DSM 9799 NC_014541 1 0 Isolated from the upper few centimeters of marine sediment of the Palma de Mallorca harbor, Spain. Aquatic-environment 12464 Fervidobacterium nodosum Rt17-B1 NC_009718 1 0 Extreme-environment 163657 Fervidobacterium pennivorans DSM 9078 NC_017095.1 1 0 isolated from a hot mud of spa in Italy. Extreme-environment 90597 Fibrella aestuarina NC_020054.1,NC_019012.1 1 1 coastal mud from the North Sea Aquatic-environment 28982 Fibrobacter succinogenes subsp. succinogenes S85 NC_013410 1 0 Rumen Terrestrial-animal-associated 203727 Fibrobacter succinogenes subsp. succinogenes S85 NC_017448.1 1 0 Rumen Terrestrial-animal-associated 43218 Filifactor alocis ATCC 35896 NC_016630 1 0 Human gingival sulcus, Virginia Clinical/Human-associated 33027 Finegoldia magna ATCC 29328 NC_010376,NC_010371 1 1 Clinical/Human-associated 12467 Flavobacteriaceae bacterium 3519-10 NC_013062 1 0 Vostok ice core, Antarctica Extreme-environment 51995 Flavobacterium branchiophilum FL-15 NC_016001 1 0 diseased sheatfish (Silurus glanis) isolated from a diseased sheatfish (Silurus glanis) in Hungary Aquatic-life-associated 202950 Flavobacterium columnare ATCC 49512 NC_016510 1 0 skin lesion of a brown trout fry, Salmo trutta Aquatic-life-associated 211628 Flavobacterium indicum GPTSA100-9 NC_017025.1 1 0 Extreme-environment 53613 Flavobacterium johnsoniae UW101 NC_009441 1 0 soil isolated from soil in England and is the type strain of this species soil 4505 Flavobacterium psychrophilum JIP02/86 NC_009613 1 0 Fish pathogen Aquatic-life-associated 174749 Flexibacter litoralis DSM 6794 NC_018018.1 1 0 Sea water aquarium outflow, La Jolla, California, U.S.A. Aquatic-environment 152299 Flexistipes sinusarabici DSM 4947 NC_015672 1 0 Brine water; Atlantis II Deep, Red Sea Aquatic-environment 147081 Fluviicola taffensis DSM 16823 NC_015321 1 0 Water of the River Taff, Cardiff, UK Aquatic-environment 142222 Francisella cf. novicida 3523 NC_017449 1 0 a foot wound sustained in brackish water in the Northern Territory of Australia Clinical/Human-associated 186347 Francisella cf. novicida Fx1 NC_017450 1 0 texas Isolated from human Clinical/Human-associated 306075 Francisella noatunensis subsp. orientalis LADL--07-285A NC_023029.1 1 0 tilapia isolated from tilapia in Costa Rica Terrestrial-animal-associated 237934 Francisella noatunensis subsp. orientalis str. Toba 04 NC_017909.1 1 0 Terrestrial-animal-associated 128299 Francisella novicida U112 NC_008601 1 0 Clinical/Human-associated 43880 Francisella philomiragia subsp. philomiragia ATCC 25017 NC_010336,NC_010331 1 2 water isolated from water in the Bear River Refuge in Utah Aquatic-environment 52793 Francisella sp. TX077308 NC_015696 1 0 Gulf of Mexico seawater samples Aquatic-environment 262051 Francisella tularensis subsp. holarctica F92 NC_019537.1 1 0 Callithrix jacchus isolated from Callithrix jacchus in 2004 in Germany Terrestrial-animal-associated 129798 Francisella tularensis subsp. holarctica FTNF002-00 NC_009749 1 0 Clinical/Human-associated 90181 Francisella tularensis subsp. holarctica LVS NC_007880 1 0 This strain (live vaccine strain) was created in the 1960's in the USA and provides protection against tularemia in animal models as well as in human Lab/Engineered 3936 Francisella tularensis subsp. holarctica OSU18 NC_008369 1 0 dead beaver isolated from a dead beaver and will be used for comparative genomics Terrestrial-animal-associated 203728 Francisella tularensis subsp. holarctica OSU18 NC_008369 1 0 Isolated from a beaver that died of tularemia in Oklahoma in 1978. Terrestrial-animal-associated 67519 Francisella tularensis subsp. mediasiatica FSC147 NC_010677 1 0 the central Asian republics of the former Soviet Union, isolated from the central Asian republics of the former Soviet Union, and is not usually associated with disease Terrestrial-animal-associated 133500 Francisella tularensis subsp. tularensis FSC198 NC_008245 1 0 mite isolated in Slovakia from a mite and is virulent in an animal model Terrestrial-animal-associated 19263 Francisella tularensis subsp. tularensis NE061598 NC_017453 1 0 Isolated in Nebraska in 1998 from the blood of a patient with ulceroglandular tularemia. human with Clinical/Human-associated disease in Nebraska Clinical/Human-associated 2086 Francisella tularensis subsp. tularensis SCHU S4 NC_006570 1 0 human case of tularemia isolated from a human case of tularemia in 1951 Clinical/Human-associated 58433 Francisella tularensis subsp. tularensis WY96-3418 NC_009257 1 0 human finger wound isolated from a human finger wound and is being sequenced for comparative genome analysis Clinical/Human-associated 196092 Francisella tularensis TI0902 NC_016937.1 1 0 dead cat Terrestrial-animal-associated 194241 Francisella tularensis TIGB03 NC_016933.1 1 0 mice Terrestrial-animal-associated 347 Frankia alni ACN14a NC_008278 1 0 green alder (Alnus crispa) growing isolated from a green alder (Alnus crispa) growing in Tadoussac, Canada Plant/agriculture-associated 10456 Frankia sp. CcI3 NC_007777 1 0 root nodules of Casuarina cunninghamiana isolated from root nodules of Casuarina cunninghamiana in 1983 at Harvard Forest Plant/agriculture-associated 51419 Frankia sp. EAN1pec NC_009921 1 0 isolated at the Kettering Research Laboratory in Ohio by M. Lalonde in 1978 Lab/Engineered 2231 Frankia sp. EuI1c NC_014666 1 0 the Autumn olive, Elaeagnus umbellata but does not form a nitrogen-fixing symbiosis isolated from the Autumn olive, Elaeagnus umbellata but does not form a nitrogen-fixing symbiosis Plant/agriculture-associated 185981 Frankia sp. QA3 NZ_CM001489.1 1 0 isolated from the root nodule of Alnus nitida Plant/agriculture-associated 162031 Frateuria aurantia DSM 6220 NC_017033.1 1 0 Lilium auratum flower, Japan Plant/agriculture-associated 132255 Fretibacterium fastidiosum NC_021038.1 1 0 Human oral isolate Clinical/Human-associated 109388 Fusobacterium nucleatum subsp. animalis 4_8 NC_021281,NC_021277 1 1 unknown 122357 Fusobacterium nucleatum subsp. nucleatum ATCC 25586 NC_003454 1 0 Clinical/Human-associated 187837 Gallibacterium anatis UMN179 NC_015460,NC_015461 1 1 isolated from an Iowa laying hen with peritonitis Terrestrial-animal-associated 53152 Gallionella capsiferriformans ES-2 NC_014394 1 0 iron contaminated groundwater in Michigan Polluted/impacted environment 61291 gamma proteobacterium HdN1 NC_014366 1 0 isolated with n-hexadeccane from German North Sea intertidal sediment. Aquatic-environment 136958 Gardnerella vaginalis 409-05 NC_013721 1 0 Clinical/Human-associated 39333 Gardnerella vaginalis ATCC 14019 NC_014644 1 0 Clinical/Human-associated 188338 Gardnerella vaginalis HMP9231 NC_017456 1 0 Clinical/Human-associated 231701 Geitlerinema sp. PCC 7407 NC_019703.1 1 0 unknown 55831 Gemmatimonas aurantiaca T-27 NC_012489 1 0 Anaerobic-aerobic sequential batch reactor under enhanced biological phosphorus removal conditions for wastewater treatment Polluted/impacted environment 81518 Geobacillus kaustophilus HTA426 NC_006510,NC_006509 1 1 deep sea sediment of the Mariana Trench isolated from deep sea sediment of the Mariana Trench in the Pacific Ocean and belongs to a closely related group of thermophilic Bacillus spp Aquatic-environment 154431 Geobacillus sp. C56-T3 NC_014206 1 0 unknown 266368 Geobacillus sp. GHH01 NC_020210.1 1 0 soil isolated from soil of Botanischer Garten Klein Flottbek, Hamburg, Germany after thermophilic enrichment for lipolytically active, thermophilic bacteria Extreme-environment 290692 Geobacillus sp. JF8 NC_022080.1,NC_022092.1 1 1 isolated from bark compost in Okayama, Japan Plant/agriculture-associated 101709 Geobacillus sp. WCH70 NC_012793,NC_012790,NC_012794 1 2 unknown 111282 Geobacillus sp. Y4.1MC1 NC_014650,NC_014651 1 1 the Bath Hot Spring isolated from the Bath Hot Spring in Yellowstone National Park Extreme-environment 94955 Geobacillus sp. Y412MC52 NC_014915,NC_014916 1 1 the Obsidian Hot Spring isolated from the Obsidian Hot Spring in Yellowstone National Park Extreme-environment 85804 Geobacillus sp. Y412MC61 NC_013411,NC_013412 1 1 the Obsidian Hot Spring isolated from the Obsidian Hot Spring in Yellowstone National Park Extreme-environment 136879 Geobacillus thermodenitrificans NG80-2 NC_009328,NC_009329 1 1 oil reservoir formation water taken at a depth of 2000 m and a temperature of 73oC isolated from oil reservoir formation water taken at a depth of 2000 m and a temperature of 73oC Extreme-environment Geobacillus thermoglucosidasius C56-YS93 NC_015660,NC_015661,NC_015665 1 2 petroleum reservoirs Extreme-environment 218498 Geobacillus thermoleovorans CCB_US3_UF5 NC_016593 1 0 Ulu Slim hot spring, Perak, Malaysia Extreme-environment 56306 Geobacter bemidjiensis Bem NC_011146 1 0 subsurface sediments collected isolated from subsurface sediments collected in Bemidji, Minnesota Aquatic-environment 31523 Geobacter lovleyi SZ NC_010814,NC_010815 1 1 Noncontaminated creek sediment in June 2002 near Seoul South Korea Aquatic-environment 55070 Geobacter metallireducens GS-15 NC_007517,NC_007515 1 1 the Potomac river downstream of Washington, DC isolated from the Potomac river downstream of Washington, DC in 1987 Aquatic-environment 137169 Geobacter sp. FRC-32 NC_011979 1 0 Uranium-contaminated subsurface at US Polluted/impacted environment 68312 Geobacter sp. M18 NC_014973 1 0 sediment Aquatic-environment 56140 Geobacter sp. M21 NC_012918 1 0 in situ uranium bioremediation experiment isolated from an in situ uranium bioremediation experiment in Rifle, Colorado, USA Polluted/impacted environment 143269 Geobacter sulfurreducens KN400 NC_017454 1 0 Electrode Elctricity producing variant Lab/Engineered 17553 Geobacter sulfurreducens PCA NC_002939 1 0 surface sediments of a hydrocarbon-contaminated ditch isolated from surface sediments of a hydrocarbon-contaminated ditch in Norman, Oklahoma Polluted/impacted environment 13052 Geobacter uraniireducens Rf4 NC_009483 1 0 Uranium bioremediation study site in Rifle Colorado Extreme-environment 49253 Geodermatophilus obscurus DSM 43160 NC_013757 1 0 soil from the Amargosa desert isolated from soil from the Amargosa desert in Nevada soil 182133 Glaciecola agarilytica 4H-3-7+YE-5 NC_015497,NC_015498 1 1 deep sea Aquatic-environment 210578 Glaciecola nitratireducens FR1064 NC_016041 1 0 seawater off Jeju Island Aquatic-environment 318133 Gloeobacter kilaueensis JS1 NC_022600.1 1 0 cave entrance Isolated from an epilithic biofilm in a lava cave in K_lauea Caldera, Hawai'i soil 86258 Gloeobacter violaceus PCC 7421 NC_005125 1 0 calcereous (chalky) rock isolated from a calcereous (chalky) rock in Switzerland soil 230752 Gloeocapsa sp. PCC 7428 NC_019745.1,NC_019747.1,NC_019759.1,NC_020051.1,NC_019746.1 1 4 moderate hot spring Extreme-environment 122154 Gluconacetobacter diazotrophicus PAl 5 NC_010125,NC_010123,NC_010124 1 2 sugarcane roots isolated from sugarcane roots in Brazil and will be used for comparative analysis Plant/agriculture-associated 203729 Gluconacetobacter diazotrophicus PAl 5 NC_011365,NC_011367 1 1 sugarcane roots isolated from sugarcane roots in Brazil and will be used for comparative analysis Plant/agriculture-associated 81109 Gluconobacter oxydans 621H NC_006677,NC_006672,NC_006673,NC_006674,NC_006675,NC_006676 1 5 unknown 258331 Gluconobacter oxydans H24 NC_019396.1,NC_019397.1 1 1 an industrial strain unknown 114338 Gordonia bronchialis DSM 43247 NC_013441,NC_013442 1 1 isolated a lung infection Clinical/Human-associated 218398 Gordonia polyisoprenivorans VH2 NC_016906.1,NC_016907.1 1 1 soil of a rubber tree plantation isolated from soil of a rubber tree plantation in Vietnam due to its effective degradation of poly(cis-1,4-isoprene) rubber Plant/agriculture-associated 50678 Gordonia sp. KTR9 NC_018581.1,NC_018582.1,NC_018583.1,NC_018580.1 1 3 Isolated from soil at an explosives testing facility. Polluted/impacted environment 38406 Gordonibacter pamelaeae 7-10-1-b NC_021021 1 0 Crohn's disease patient Clinical/Human-associated 5527 Gramella forsetii KT0803 NC_008571 1 0 Concentrated seawater collected from the German Bight in the North Sea Aquatic-environment 83793 Granulibacter bethesdensis CGDNIH1 NC_008343 1 0 39 year old man with Chronic granulomatous disease Clinical/Human-associated 133973 Haemophilus ducreyi 35000HP NC_002940 1 0 human passage derivative This strain is a human passage derivative of Haemophilus ducreyi strain 35000 that is serum-resistant. Clinical/Human-associated 165663 Haemophilus influenzae 10810 NC_016809 1 0 a case of meningitis Clinical/Human-associated 100748 Haemophilus influenzae 86-028NP NC_007146 1 0 pediatric patient with otitis media from Columbus Children's Hospital isolate from a pediatric patient with otitis media from Columbus Children's Hospital Clinical/Human-associated 165906 Haemophilus influenzae F3031 NC_014920 1 0 Brazilian purpuric fever outbreak in the early 1980s Clinical/Human-associated 177079 Haemophilus influenzae F3047 NC_014922 1 0 Brazilian purpuric fever outbreak in the early 1980s Clinical/Human-associated 313847 Haemophilus influenzae KR494 NC_022356 1 0 patient suffering from sepsis and necrotizing myositis Clinical/Human-associated 81350 Haemophilus influenzae PittEE NC_009566 1 0 middle-ear effusion isolate recovered by Dr Robert Wadowsky from the middle-ear effusion of a child in Pittsburgh who was undergoing tympanostomy and ventilation tube placement for the treatment of chronic otitis media with effusion (COME). Clinical/Human-associated 102487 Haemophilus influenzae PittGG NC_009567 1 0 external ear discharge isolate recovered by Dr Robert Wadowsky from the external ear discharge of a spontaneously perforated tympanic membrane of a child in Pittsburgh who had been diagnosed with otorrhea. Clinical/Human-associated 30952 Haemophilus influenzae R2846 NC_017452 1 0 middle ear fluid of a child with acute otitis media isolated from middle ear fluid of a child with acute otitis media Clinical/Human-associated 103652 Haemophilus influenzae R2866 NC_017451 1 0 the blood of a child with meningitis isolated from the blood of a child with meningitis Clinical/Human-associated 48452 Haemophilus influenzae Rd KW20 NC_000907 1 0 Lab/Engineered 168133 Haemophilus parainfluenzae T3T1 NC_015964 1 0 obtained from the throat of a healthy child Clinical/Human-associated 127548 Haemophilus parasuis SH0165 NC_011852 1 0 isolated from a Glasser's disease outbreak farm Terrestrial-animal-associated 288875 Haemophilus parasuis ZJ0906 NC_021521.1 1 0 isolated from a Glasser's diseased pig Terrestrial-animal-associated 53361 Haemophilus somnus 129PT NC_008309,NC_006298 1 1 bovine urogenital tract Terrestrial-animal-associated 93646 Haemophilus somnus 2336 NC_010519 1 0 the lung of a calf which had pneumonia isolated from the lung of a calf which had pneumonia Terrestrial-animal-associated 29232 Hahella chejuensis KCTC 2396 NC_007645 1 0 Marine sediment from Cheju Island, Republic of Korea Aquatic-environment 106773 Halanaerobium praevalens DSM 2228 NC_017455 1 0 Isolated from the hypersaline surface sediments of Great Salt Lake, Utah, USA. surface sediments of a saline lake Extreme-environment 157090 Halanaerobium sp. 'sapolanicus' NC_014654 1 0 haloalkaline, anaerobic sediments of Soap Lake Extreme-environment 22000 Haliangium ochraceum DSM 14365 NC_013440 1 0 seaweed collected from a sandy beach isolated from seaweed collected from a sandy beach in Kanagawa, Japan Plant/agriculture-associated 147579 Haliscomenobacter hydrossis DSM 1100 NC_015510,NC_015513,NC_015512,NC_015511 1 3 sludge (activated sludge, Oss) Polluted/impacted environment 165146 Halobacillus halophilus DSM 2266 NC_017668.1,NC_017670.1,NC_017669.1 1 2 salt marsh soil soil 149681 Halobacteroides halobius DSM 5150 NC_019978.1 1 0 Dead Sea sediment Aquatic-environment 161731 Halomonas elongata DSM 2581 NC_014532 1 0 solar salt facility isolated from a solar salt facility and is halotolerant up to a concentration of 35% Extreme-environment 112047 Halorhodospira halophila SL1 NC_008789 1 0 salt lake mud isolated from salt lake mud and will be used for comparative analysis with other halophilic organisms Extreme-environment 5373 Halothece sp. PCC 7418 NC_019779.1 1 0 Water, lake, Solar lake Extreme-environment 56292 Halothermothrix orenii H 168 NC_011899 1 0 the sediment of a salt lake isolated from the sediment of a salt lake in Tunisia Extreme-environment 120669 Halothiobacillus neapolitanus c2 NC_013422 1 0 Disintegrated concrete in outfall sewer of Melbourne south east sewerage system, Australia Polluted/impacted environment Halyomorpha halys symbiont NC_022547 1 0 Endosymbiont Insect-associated/other symbiont 71660 Helicobacter acinonychis str. Sheeba NC_008229,NC_008230 1 1 isolated from a biopsy of a Russian circus lion with gastroenteritis Terrestrial-animal-associated Helicobacter bizzozeronii CIII-1 NC_015674,NC_015670 1 1 The only nonpylori Helicobacter species isolated from human gastric biopsy tissue. Isolated in March 2008 from corpus biopsy tissue of a 45-year-old female patient with severe gastric symptoms. Clinical/Human-associated 232860 Helicobacter cetorum MIT 00-7128 NC_017737.1,NC_017738.1 1 1 beluga whale from Mystic Aquarium isolate from beluga whale from Mystic Aquarium in Connecticut Terrestrial-animal-associated 236126 Helicobacter cetorum MIT 99-5656 NC_017735.1,NC_017736.1 1 1 stranded wild Atlantic white-sided dolphin isolate from stranded wild Atlantic white-sided dolphin Terrestrial-animal-associated 248530 Helicobacter cinaedi ATCC BAA-847 NC_020555.1 1 0 rectal swab rectal swab Clinical/Human-associated Helicobacter cinaedi PAGU611 NC_017761,NC_017762 1 1 Isolated in a case of human bacteremia. Clinical/Human-associated 178703 Helicobacter felis ATCC 49179 NC_014810 1 0 gastric mucosa of adult cat Terrestrial-animal-associated 257179 Helicobacter heilmannii ASB1.4 NC_019674 1 0 kitten isolate ASB1 from a kitten with severe gastritis. Terrestrial-animal-associated 90276 Helicobacter hepaticus ATCC 51449 NC_004917 1 0 Liver Liver Terrestrial-animal-associated 149082 Helicobacter mustelae 12198 NC_013949 1 0 Ferrets Terrestrial-animal-associated 182737 Helicobacter pylori 2017 NC_017374 1 0 Recovered after a decade of the original isolation of the parent strain from a West African duodenal ulcer disease patient in France. West African, duodenal ulcer disease patient in France Clinical/Human-associated 183925 Helicobacter pylori 2018 NC_017381 1 0 Recovered after a decade of the original isolation of the parent strain from a West African duodenal ulcer disease patient in France. est African, duodenal ulcer disease patient in France Clinical/Human-associated 33062 Helicobacter pylori 26695 NC_000915 1 0 patient isolated from a patient in the United Kingdom who had gastritis before 1987, this strain has undergone repeated subculturing prior to being sequenced Clinical/Human-associated Helicobacter pylori 26695 NC_018939 1 0 originally isolated from a patient Clinical/Human-associated 62423 Helicobacter pylori 35A NC_017360 1 0 Clinical/Human-associated 144621 Helicobacter pylori 51 NC_017382 1 0 duodenal ulcer patient who had undergone a gastrointestinal examination isolated from a duodenal ulcer patient who had undergone a gastrointestinal examination in a hospital in South Korea Clinical/Human-associated 145372 Helicobacter pylori 52 NC_017354 1 0 Isolated in south korea Clinical/Human-associated 75410 Helicobacter pylori 83 NC_017375 1 0 Clinical/Human-associated 166603 Helicobacter pylori 908 NC_017357 1 0 African patient living in France, who suffered from duodenal ulcer disease Clinical/Human-associated 233131 Helicobacter pylori Aklavik117 NC_019560.1,NC_019562.1,NC_019561.1 1 2 Amerindian Clinical/Human-associated isolate from Amerindian resident in Aklavik, Canada Clinical/Human-associated 228384 Helicobacter pylori Aklavik86 NC_019563.1,NC_019564.1,NC_019565.1 1 2 Amerindian Clinical/Human-associated isolate from Amerindian resident in Aklavik, Canada Clinical/Human-associated 144313 Helicobacter pylori B38 NC_012973 1 0 isolated from a 62-year-old man suffering from MALT lymphoma Clinical/Human-associated 164240 Helicobacter pylori B8 NC_014256,NC_014257 1 0 human gastric ulcer patient Clinical/Human-associated 306514 Helicobacter pylori BM012A NC_022886.1 1 0 antral gastric biopsy specimens antral gastric biopsy specimens were taken from human volunteers during gastroendoscopy Clinical/Human-associated 306851 Helicobacter pylori BM012S NC_022911.1 1 0 antral gastric biopsy specimens antral gastric biopsy specimens were taken from human volunteers during gastroendoscopy Clinical/Human-associated 160354 Helicobacter pylori Cuz20 NC_017358 1 0 Amerindian resident of the remote Amerindian village from Monte Carmelo near Cuzco, Peru isolated from an Amerindian resident of the remote Amerindian village from Monte Carmelo near Cuzco, Peru Clinical/Human-associated 237915 Helicobacter pylori ELS37 NC_017063.1,NC_017064.1 1 1 gastric cancer patient from El Salvador rural area isolate from gastric cancer patient from El Salvador rural area Clinical/Human-associated 167340 Helicobacter pylori F16 NC_017368 1 0 Isolated from patients with gastritis in Fukui, Japan. patient with gastritis Clinical/Human-associated 168700 Helicobacter pylori F30 NC_017365,NC_017369 1 1 Isolated from patients with duodenal ulcer in Fukui, Japan. Patient with duodenal ulcer Clinical/Human-associated 176079 Helicobacter pylori F32 NC_017366,NC_017370 1 1 patients with diffuse type gastric cancer Clinical/Human-associated 165399 Helicobacter pylori F57 NC_017367 1 0 Isolated from patients with diffuse type gastric cancer in Fukui, Japan. patients with diffuse type gastric cancer Clinical/Human-associated 113476 Helicobacter pylori G27 NC_011333,NC_011334 1 1 isolated from an endoscopy patient from Grosseto Hospital Clinical/Human-associated 173289 Helicobacter pylori Gambia94/24 NC_017371,NC_017364 1 1 Clinical/Human-associated 56048 Helicobacter pylori HPAG1 NC_008086,NC_008087 1 1 Swedish patient with chronic atrophic gastritis, the precursor to gastric adenocarcinoma isolated from a Swedish patient with chronic atrophic gastritis, the precursor to gastric adenocarcinoma Clinical/Human-associated 238509 Helicobacter pylori HUP-B14 NC_017733.1,NC_017734.1 1 1 resident of Spain isolate from resident of Spain Clinical/Human-associated 171055 Helicobacter pylori India7 NC_017372 1 0 Clinical/Human-associated 98156 Helicobacter pylori J99 NC_000921 1 0 patient with duodenal ulcer isolated in 1994 in the USA from a patient with duodenal ulcer Clinical/Human-associated 170489 Helicobacter pylori Lithuania75 NC_017362,NC_017363 1 1 isolated in Lithuania Clinical/Human-associated 282511 Helicobacter pylori OK113 NC_020508.1 1 0 Clinical/Human-associated 280656 Helicobacter pylori OK310 NC_020509.1,NC_020556.1 1 1 Clinical/Human-associated 2824 Helicobacter pylori P12 NC_011498,NC_011499 1 1 patient with duodenal ulcer isolate obtained from a patient with duodenal ulcer Clinical/Human-associated 227703 Helicobacter pylori PeCan18 NC_017742.1 1 0 gastric antrum from resident of Lima, Peru isolate from gastric antrum from resident of Lima, Peru Clinical/Human-associated 173672 Helicobacter pylori PeCan4 NC_014555,NC_014556 1 1 Peruvian gastric cancer patient isolated from a Peruvian gastric cancer patient Clinical/Human-associated 210577 Helicobacter pylori Puno120 NC_017378,NC_017377 1 1 Amerindian gastritis patient Clinical/Human-associated 214951 Helicobacter pylori Puno135 NC_017379 1 0 Clinical/Human-associated isolate from gastric antrum from Amerindian resident of Puno region in Peru Clinical/Human-associated 261100 Helicobacter pylori Rif1 NC_018937.1 1 0 Lab/Engineered 259963 Helicobacter pylori Rif2 NC_018938.1 1 0 Lab/Engineered 215244 Helicobacter pylori Santal49 NC_017376.1,NC_017380.1 1 1 Clinical/Human-associated 163788 Helicobacter pylori Sat464 NC_017359,NC_017356 1 1 Amerindian resident from Satipo region, Peru Pure culture of strain from Amerindian resident from Satipo region, Peru Clinical/Human-associated 237387 Helicobacter pylori Shi112 NC_017741.1 1 0 Clinical/Human-associated 234201 Helicobacter pylori Shi169 NC_017740.1 1 0 Clinical/Human-associated 236571 Helicobacter pylori Shi417 NC_017739.1 1 0 Clinical/Human-associated 23559 Helicobacter pylori Shi470 NC_010698 1 0 gastric antrum from Amerindian resident of remote Amazonian village of Shimaa, Peru isolate from gastric antrum from Amerindian resident of remote Amazonian village of Shimaa, Peru Clinical/Human-associated 169273 Helicobacter pylori SJM180 NC_014560 1 0 Amerindian resident of San Juan Miraflores shantytown isolated from an Amerindian resident of San Juan Miraflores shantytown in Lima Peru with gastritis Clinical/Human-associated 310127 Helicobacter pylori SouthAfrica20 NC_022130.1 1 0 stomach Clinical/Human-associated 171460 Helicobacter pylori SouthAfrica7 NC_017361,NC_017373 1 1 South african San societies Clinical/Human-associated 287694 Helicobacter pylori UM032 NC_021215.1 1 0 biospy sample from patient Clinical/Human-associated 293193 Helicobacter pylori UM037 NC_021217.1 1 0 biospy sample from patient Clinical/Human-associated 298878 Helicobacter pylori UM066 NC_021218.1 1 0 biospy sample from patient Clinical/Human-associated 297786 Helicobacter pylori UM298 NC_021882.1 1 0 gastric tissue Terrestrial-animal-associated 289387 Helicobacter pylori UM299 NC_021216.1 1 0 biopsy sample Terrestrial-animal-associated 5358 Helicobacter pylori v225d NC_017355,NC_017383 1 1 Isolated from a gastric antral biopsy specimen from a Piaroa Amerindian who underwent a gastroscopy and was found to have acute superficial gastritis. Helicobacter pylori v225 is an Amerindian strain obtained from a Piaroa Amerindian with acute superficial gastritis. Clinical/Human-associated 228972 Helicobacter pylori XZ274 NC_017926.1,NC_017919.1 1 1 female Tibetan gastric cancer patient's stomach isolated from a female Tibetan gastric cancer patient's stomach in China Clinical/Human-associated 36755 Heliobacterium modesticaldum Ice1 NC_010337 1 0 hot spring microbial mats and volcanic soil in Iceland Extreme-environment 153339 Herbaspirillum seropedicae SmR1 NC_014323 1 0 Roots of rice plants Plant/agriculture-associated 17568 Herminiimonas arsenicoxydans NC_009138 1 0 heavy metal contaminated sludge from an industrial water treatment plant isolated from heavy metal contaminated sludge from an industrial water treatment plant Polluted/impacted environment 93466 Herpetosiphon aurantiacus ATCC 23779 NC_009972,NC_009974,NC_009973 1 2 Birch Lake, Minnesota isolated from Birch Lake in Minnesota Aquatic-environment 155866 Hippea maritima DSM 10411 NC_015318 1 0 Marine sediment from hot vent of tidal zone; Papua New Guinea, Matupi Harbour Extreme-environment 9878 Hirschia baltica ATCC 49814 NC_012982,NC_012983 1 1 brackish water Aquatic-environment 36152 Hydrogenobacter thermophilus TK-6 NC_013799 1 0 Soil near hot-spring in Izu Peninsula, Japan Extreme-environment 203733 Hydrogenobacter thermophilus TK-6 NC_017161 1 0 strain derived from original strain isolated at hot-spring in Izu Peninsula, Japan Extreme-environment 15522 Hydrogenobaculum sp. 3684 NC_011126 1 0 Dragon spring, an acid-sulfate-chloride geothermal spring at Yellowstone National Park Extreme-environment 90430 Hydrogenobaculum sp. HO NC_020411.1 1 0 fresh water Acidic geothermal spring sediment, Yellowstone National Park Extreme-environment 5595 Hydrogenobaculum sp. SN NC_020814.1 1 0 solated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY Extreme-environment 64203 Hydrogenobaculum sp. Y04AAS1 NC_011126 1 0 Obsidian Pool, Acidic hot spring in Yellowstone National Park Extreme-environment 91677 Hyphomicrobium denitrificans ATCC 51888 NC_014313 1 0 unknown 176985 Hyphomicrobium sp. MC1 NC_015717 1 0 isolated from industrial sewage Polluted/impacted environment 17450 Hyphomonas neptunium ATCC 15444 NC_008358 1 0 seawater Aquatic-environment 288866 Idiomarina loihiensis GSL 199 NC_021286.1 1 0 isolated form the hypersaline north arm of Great Salt Lake UT Extreme-environment 21852 Idiomarina loihiensis L2TR NC_006512 1 0 hydrothermal vent at a depth of 1300 m from the Lo'ihi Seamount southeast of Hawaii isolated from a hydrothermal vent at a depth of 1300 m from the Lo'ihi Seamount southeast of Hawaii Extreme-environment 177444 Ignavibacterium album JCM 16511 NC_017464.1 1 0 Hot spring, Yumata, Nagano, Japan Extreme-environment 282115 Ilumatobacter coccineum YM16-304 NC_020520.1 1 0 sample of seashore sand using media with an artificial seawater base Aquatic-environment 34265 Ilyobacter polytropus DSM 2926 NC_014632,NC_014633,NC_014634 1 2 Marine anoxic mud from Cuxhaven, Germany Aquatic-environment 153415 Intrasporangium calvum DSM 43043 NC_014830 1 0 Air in a school dining room unknown 162825 Isoptericola variabilis 225 NC_015588 1 0 hindgut of Australian termite Insect-associated/other symbiont 14453 Isosphaera pallida ATCC 43644 NC_014957,NC_014962 1 1 algal mat from Kah-nee-tah Hot Spring in Oregon Extreme-environment 43325 Jannaschia sp. CCS1 NC_007802,NC_007801 1 1 isolated from Pacific coastal seawater, Bodega Head, CA Aquatic-environment 106498 Janthinobacterium sp. Marseille NC_009659 1 0 solution used in kidney dialysis isolated from a solution used in kidney dialysis Clinical/Human-associated 9837 Jonesia denitrificans DSM 20603 NC_013174 1 0 boiled ox blood isolated from boiled ox blood Terrestrial-animal-associated 123990 Kangiella koreensis DSM 16069 NC_013166 1 0 the tidal flats of the Yellow Sea isolated from the tidal flats of the Yellow Sea in Korea Aquatic-environment 170732 Ketogulonicigenium vulgare Y25 NC_014621,NC_014625,NC_014626 1 2 vitamin C production facilty Production-site-facility 151953 Ketogulonicigenium vulgarum WSH-001 NC_017384,NC_017386,NC_017385 1 2 vitamin C production facilty industrial isolate Production-site-facility 28154 Kineococcus radiotolerans SRS30216 NC_009664,NC_009806,NC_009660 1 2 high-level radioactive waste cell at the Savannah River Site isolated from a high-level radioactive waste cell at the Savannah River Site in Aiken, South Carolina, USA, in 2002 Polluted/impacted environment 84808 Kitasatospora setae KM-6054 NC_016109 1 0 soil isolated from soil in Japan soil 249058 Klebsiella oxytoca E718 NC_018106,NC_018107,NC_021501 1 2 patient underwent renal transplantation isolated in 2010, from a patient underwent renal transplantation in China then presented to a hospital in Taiwan 7 days later Clinical/Human-associated 189366 Klebsiella oxytoca KCTC 1686 NC_016612 1 0 obtained from the Korean Collection for Type Culture (Daejun, South Korea). unknown 121904 Klebsiella pneumoniae 342 NC_011283,NC_011281,NC_011282 1 2 the stem tissue of Zea mays isolated from the stem tissue of Zea mays Plant/agriculture-associated 260969 Klebsiella pneumoniae CG43 NC_022566.1 1 0 liver abscess Clinical/Human-associated 315144 Klebsiella pneumoniae JM45 NC_022082.1,NC_022078.1,NC_022083.1 1 2 72-year-old male with cerebral infarction after colon carcinoma resection isolated another carbapenem-resistant K. pneumoniae strain and then performed bacteriological experiments, PCR and whole-genome sequencing Clinical/Human-associated 211346 Klebsiella pneumoniae KCTC 2242 NC_017540,NC_017541 1 1 unknown 243659 Klebsiella pneumoniae subsp. pneumoniae 1084 NC_018522.1 1 0 Clinical/Human-associated 218548 Klebsiella pneumoniae subsp. pneumoniae HS11286 NC_016845,NC_016838,NC_016846,NC_016839,NC_016840,NC_016847,NC_016841 1 6 human sputum in 2011 in Shanghai, China Clinical/Human-associated 13394 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 NC_009648,NC_009650,NC_009651,NC_009652,NC_009653,NC_009649 1 5 patient isolated from a patient in 1994 Clinical/Human-associated 21779 Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 NC_012731,NC_006625 1 1 liver abscess isolated from a liver abscess and will be used for comparative analysis Clinical/Human-associated 82009 Klebsiella pneumoniae subsp. rhinoscleromatis SB3432 NC_021232.1,NC_021231.1 1 1 isolated in 2004 in the Avicenne hospital, Bobigny, France from a biopsy of the left nasal cavity of an 11-year old patient diagnosed with rhinoscleroma Clinical/Human-associated 54872 Klebsiella variicola At-22 NC_013850 1 0 fungus gardens of 80 leaf-cutter ant colonies Insect-associated/other symbiont 5258 Kocuria rhizophila DC2201 NC_010617 1 0 soil soil 109242 Kosmotoga olearia TBF 19.5.1 NC_012785 1 0 oil deposit isolated from an oil deposit Extreme-environment 67707 Kribbella flavida DSM 17836 NC_013729 1 0 soil isolated from soil in China soil 190710 Krokinobacter diaphorus 4H-3-7-5 NC_015496 1 0 subseafloor sediments at Suruga Bay (Japan) from a depth of 31.4 meters Aquatic-environment 29608 Kyrpidia tusciae DSM 2912 NC_014098 1 0 at Naples Solfatara (volcano) in Italy Extreme-environment 14067 Kytococcus sedentarius DSM 20547 NC_013169 1 0 Marine Aquatic-environment 192204 Lacinutrix sp. 5H-3-7-4 NC_015638 1 0 subseafloor sediments at Suruga Bay (Japan) from a depth of 41 m Aquatic-environment 171603 Lactobacillus acidophilus 30SC NC_015214,NC_015218,NC_015213 1 2 swine intestine showing strong acid tolerance and bile resistance isolated from swine intestine showing strong acid tolerance and bile resistance Terrestrial-animal-associated 285259 Lactobacillus acidophilus La-14 NC_021181.1 1 0 unknown 7974 Lactobacillus acidophilus NCFM NC_006814 1 0 human isolated from a human in 1970 and characterized at North Caroline State University Clinical/Human-associated 150400 Lactobacillus amylovorus GRL 1112 NC_014724,NC_015322,NC_015319 1 2 porcine faeces isolated from porcine faeces Terrestrial-animal-associated 156066 Lactobacillus amylovorus GRL1118 NC_017470,NC_017471,NC_017472 1 2 the pig intestine (ileum) isolated from the pig intestine (ileum) Terrestrial-animal-associated 134470 Lactobacillus brevis ATCC 367 NC_008497,NC_008498,NC_008499 1 2 Lab/Engineered 187236 Lactobacillus brevis KB290 NC_020819.1,NC_020826.1,NC_020822.1,NC_020821.1,NC_020820.1,NC_020824.1,NC_020827.1,NC_020823.1,NC_020828.1,NC_020825.1 1 9 traditional Japanese fermented vegetable traditional Japanese fermented vegetable Food-associated 228279 Lactobacillus buchneri CD034 NC_018610.1,NC_018611.1 1 1 stable grass silage Isolated from stable grass silage in Austria Plant/agriculture-associated 105504 Lactobacillus buchneri NRRL B-30929 NC_015421,NC_015428,NC_015429,NC_015420 1 3 fuel ethanol production facility isolated from a fuel ethanol production facility Production-site-facility 62221 Lactobacillus casei ATCC 334 NC_008526,NC_008502 1 1 Emmental cheese isolated from Emmental cheese and will be used for comparative analysis Food-associated 184581 Lactobacillus casei BD-II NC_017474,NC_017476 1 1 homemade koumiss isolated from homemade koumiss in China Food-associated 89204 Lactobacillus casei BL23 NC_010999 1 0 cheese isolated from cheese and will be used for comparative analysis Food-associated 186771 Lactobacillus casei LC2W NC_017473,NC_017475 1 1 traditional dairy products isolated from traditional dairy products in Inner Mongolia, China Food-associated 317710 Lactobacillus casei LOCK919 NC_021721.1,NC_021722.1 1 1 isolated from child feces Clinical/Human-associated 45142 Lactobacillus casei str. Zhang NC_011352,NC_014334 1 1 traditional home-made koumiss (fermented mare's milk) isolated from traditional home-made koumiss (fermented mare's milk) in Inner Mongolia, China Food-associated 261497 Lactobacillus casei W56 NC_018641.1,NC_020057.1 1 1 probiotic products ingredient of commercially available probiotic products Food-associated 149433 Lactobacillus crispatus ST1 NC_014106 1 0 the crop of chickens, displays a strong protein-dependent adhesion to the epithelial cells of human vagina isolated from the crop of chickens, displays a strong protein-dependent adhesion to the epithelial cells of human vagina Terrestrial-animal-associated 183177 Lactobacillus delbrueckii subsp. bulgaricus 2038 NC_017469 1 0 industrial strain used by Meiji Dairies Corporation originally isolated from Bulgaria Production-site-facility 123523 Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 NC_008054 1 0 Bulgarin yoghurt Food-associated 70259 Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 NC_008529 1 0 derived from an existing strain (derived from a French starter culture; CHCC757) Lab/Engineered 160915 Lactobacillus delbrueckii subsp. bulgaricus ND02 NC_014727,NC_014728 1 1 traditional dairy products of minority nationalities isolated from traditional dairy products of minority nationalities in China and will be used for comparative analysis with other Lactobacillus species Food-associated 149467 Lactobacillus fermentum CECT 5716 NC_017465 1 0 human milk and has antimicrobial, anti-inflammatory, and immunomodulatory properties, both isolated from human milk and has antimicrobial, anti-inflammatory, and immunomodulatory properties, both in vitro and in vivo Clinical/Human-associated 160585 Lactobacillus fermentum F-6 NC_021235.1 1 0 traditional dairy products of minority nationalities isolated from traditional dairy products of minority nationalities in China, and has some good probiotic properties such as high resistance to acidic pH, bile salt and antibacterial activity Food-associated 15497 Lactobacillus fermentum IFO 3956 NC_010610 1 0 fermented plant material in Japan Food-associated 62225 Lactobacillus gasseri ATCC 33323 NC_008530 1 0 human human isolate and is the type strain Clinical/Human-associated 90723 Lactobacillus helveticus CNRZ32 NC_021744.1 1 0 Food-associated 91643 Lactobacillus helveticus DPC 4571 NC_010080 1 0 a Swiss cheese isolate Food-associated 162941 Lactobacillus helveticus H10 NC_017467,NC_017468 1 1 traditional dairy products of minority nationalities isolated from traditional dairy products of minority nationalities in China Food-associated 171132 Lactobacillus johnsonii DPC 6026 NC_017477 1 0 porcine intestinal tract Terrestrial-animal-associated 137736 Lactobacillus johnsonii FI9785 NC_013504,NC_013505,NC_012552 1 2 poultry derived from poultry Terrestrial-animal-associated 315565 Lactobacillus johnsonii N6.2 NC_022909.1 1 0 diabetes resistant rats Terrestrial-animal-associated 1832 Lactobacillus johnsonii NCC 533 NC_005362 1 0 the Nestle strain collection isolate from the Nestle strain collection Production-site-facility 189943 Lactobacillus kefiranofaciens ZW3 NC_015602,NC_015603,NC_015598 1 2 traditional dairy product Kefir Grain in Tibet, China Food-associated 232155 Lactobacillus pentosus KCA1 NZ_CM001538.1 1 0 human vagina, Nigerian woman Isolated from human vagina, Nigerian woman Clinical/Human-associated 297737 Lactobacillus plantarum 16 NC_021514.1,NC_021528.1,NC_021527.1,NC_021520.1,NC_021518.1,NC_021517.1,NC_021516.1,NC_021515.1,NC_021519.1,NC_021525.1,NC_021526.1 1 10 isolated during a large scale screen to identify lactic acid bacterial strains with antifungal activitites Polluted/impacted environment 68346 Lactobacillus plantarum JDM1 NC_012984 1 0 Lab/Engineered 164449 Lactobacillus plantarum subsp. plantarum P-8 NC_021224.1,NC_021227.1,NC_021228.1,NC_021226.1,NC_021225.1,NC_021233.1,NC_021234.1 1 6 plant material, and the gastrointestinal tract of animals isolated from plant material, and the gastrointestinal tract of animals Plant/agriculture-associated 173910 Lactobacillus plantarum subsp. plantarum ST-III NC_014554,NC_014558 1 1 isolated from kimchi Food-associated 27411 Lactobacillus plantarum WCFS1 NC_004567,NC_006375,NC_006376,NC_006377 1 3 human saliva isolated from human saliva Clinical/Human-associated 275832 Lactobacillus plantarum ZJ316 NC_020229.1 1 0 healthy newborn fecal sample isolated from health infant fecal samples, has many probiotic properties, such as significant improvement of pig growth and pork quality, and antimicrobial activity against various pathogens in vitro, such as Micrococcus luteus, Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Salmonella enterica, Listeria monocytogenes, and others Clinical/Human-associated 87937 Lactobacillus reuteri DSM 20016 NC_009513 1 0 human isolate human isolate Clinical/Human-associated 296600 Lactobacillus reuteri I5007 NC_021494.1,NC_021504.1,NC_021497.1,NC_021498.1,NC_021503.1,NC_021496.1,NC_021495.1 1 6 healthy weaning piglets isolated from the colonic mucosa of healthy weaning piglets in Beijing, China Terrestrial-animal-associated 111271 Lactobacillus reuteri JCM 1112 NC_010609 1 0 the intestine of an adult human isolated from the intestine of an adult human Clinical/Human-associated 316352 Lactobacillus reuteri TD1 NC_021872.1 1 0 isolated from a type 1 diabetes-resistant rat model Terrestrial-animal-associated 212963 Lactobacillus rhamnosus ATCC 8530 NC_017491 1 0 beer Food-associated 2892 Lactobacillus rhamnosus GG NC_013198 1 0 intestinal Clinical/Human-associated 203734 Lactobacillus rhamnosus GG NC_017482 1 0 healthly human intestinal flora isolated from healthly human intestinal flora Clinical/Human-associated 58455 Lactobacillus rhamnosus Lc 705 NC_013199,NC_013200 1 1 industrial isolate Production-site-facility 308714 Lactobacillus rhamnosus LOCK900 NC_021723.1 1 0 isolated from feces of a healthy 26-year-old woman Terrestrial-animal-associated 299904 Lactobacillus rhamnosus LOCK908 NC_021725.1 1 0 isolated from the feces of a healthy 6-year-old girl Terrestrial-animal-associated 210878 Lactobacillus ruminis ATCC 27782 NC_015975.1 1 0 bovine isolate Terrestrial-animal-associated 116432 Lactobacillus sakei subsp. sakei 23K NC_007576 1 0 French sausage isolated from a French sausage Food-associated 150030 Lactobacillus salivarius CECT 5713 NC_017481,NC_017479,NC_017480,NC_017499 1 3 human milk and has antimicrobial, anti-inflammatory, and immunomodulatory properties, both isolated from human milk and has antimicrobial, anti-inflammatory, and immunomodulatory properties, both in vitro and in vivo Clinical/Human-associated 43464 Lactobacillus salivarius UCC118 NC_007929,NC_006530,NC_007930,NC_006529 1 3 the human gastrointestinal tract isolated from the human gastrointestinal tract Clinical/Human-associated 150155 Lactobacillus sanfranciscensis TMW 1.1304 NC_015978,NC_015979,NC_015980 1 2 Isolated in 2006 from a commercial mother sponge (sourdough starter) with a tradition of continuous propagation. isolated from an industrial sourdough fermentation Food-associated 43052 Lactococcus garvieae ATCC 49156 NC_015930 1 0 fish isolate Aquatic-life-associated 33577 Lactococcus garvieae Lg2 NC_017490 1 0 fish isolate Aquatic-life-associated 226133 Lactococcus lactis subsp. cremoris A76 NC_017492,NC_017497,NC_017495,NC_017493,NC_017496 1 4 dairy strain isolated from a cheese production outfit in 1965 Production-site-facility 316987 Lactococcus lactis subsp. cremoris KW2 NC_022369.1 1 0 fermented corn and used to compare with dairy starter cultures isolated from fermented corn and used to compare with dairy starter cultures Food-associated 4574 Lactococcus lactis subsp. cremoris MG1363 NC_009004 1 0 Food-associated 151604 Lactococcus lactis subsp. cremoris NZ9000 NC_017949.1 1 0 Food-associated 38071 Lactococcus lactis subsp. cremoris SK11 NC_008527,NC_008503,NC_008504,NC_008505,NC_008506,NC_008507 1 5 Food-associated 226677 Lactococcus lactis subsp. cremoris UC509.9 NC_019435.1 1 0 Irish Dairy Production-site-facility 178659 Lactococcus lactis subsp. lactis CV56 NC_017486,NC_017483,NC_017487,NC_017484,NC_017485,NC_017488 1 5 Human vagina Clinical/Human-associated 136773 Lactococcus lactis subsp. lactis Il1403 NC_002662 1 0 derivative of strain IL594 isolated from a cheese starter culture. derivative of strain IL594 isolated from a cheese starter culture. Production-site-facility 225240 Lactococcus lactis subsp. lactis IO-1 NC_020450.1 1 0 water in kitchen sink drain pit water in kitchen sink drain pit Polluted/impacted environment 141273 Lactococcus lactis subsp. lactis KF147 NC_013656,NC_013657 1 1 Plant/agriculture-associated 318245 Lactococcus lactis subsp. lactis KLDS 4.0325 NC_022593.1,NC_022587.1 1 1 home-made koumiss isolated from home made koumiss in Sinkiang of China Food-associated 49832 Laribacter hongkongensis HLHK9 NC_012559 1 0 case of gastroenteritis isolated from a case of gastroenteritis in Hong Kong and will be used for comparative analysis Clinical/Human-associated 265757 Lawsonia intracellularis N343 NC_020127.1,NC_020128.1,NC_020129.1,NC_020130.1 1 3 the ileum of a sow that died of haemorrhagic diarrhoea isolated from the ileum of a sow that died of haemorrhagic diarrhoea Terrestrial-animal-associated 40445 Lawsonia intracellularis PHE/MN1-00 NC_008011,NC_008012,NC_008013,NC_008014 1 3 intestinal mucosal lesions isolated from intestinal mucosal lesions in pigs that had proliferative enteropathy (PE) Terrestrial-animal-associated 116579 Leadbetterella byssophila DSM 17132 NC_014655 1 0 isolated from cotton-waste compost soil Polluted/impacted environment 159544 Legionella longbeachae NSW150 NC_014544,NC_013861 1 1 Clinical/Human-associated Legionella longbeachae NSW150 NC_013861,NC_014544 1 1 Clinically isolated in Australia. Clinical/Human-associated 70474 Legionella pneumophila 2300/99 Alcoy NC_014125 1 0 patient affected isolated from a patient affected by legionellosis in Alcoy (Spain) Clinical/Human-associated 45588 Legionella pneumophila str. Corby NC_009494 1 0 human isolate human isolate Clinical/Human-associated 33733 Legionella pneumophila str. Lens NC_006369,NC_006366 1 1 Clinical/Human-associated 27771 Legionella pneumophila str. Paris NC_006368,NC_006365 1 1 Clinical/Human-associated 178567 Legionella pneumophila subsp. pneumophila ATCC 43290 NC_016811 1 0 Clinical/Human-associated isolate from the Colorado Department of Health, Denver, CO. Clinical/Human-associated Legionella pneumophila subsp. pneumophila HL06041035 NC_018140 1 0 isolated from a hospital water system since over 10 years Polluted/impacted environment 279871 Legionella pneumophila subsp. pneumophila LPE509 NC_020521.1,NC_020522.1 1 1 Clinical/Human-associated 206247 Legionella pneumophila subsp. pneumophila str. Hextuple_2q NC_017525.1 1 0 mutant organism Lab/Engineered 204708 Legionella pneumophila subsp. pneumophila str. Hextuple_3a NC_017526.1 1 0 mutant organism Lab/Engineered 122099 Legionella pneumophila subsp. pneumophila str. Lorraine NC_018139.1,NC_018141.1 1 1 Clinical/Human-associated 29832 Legionella pneumophila subsp. pneumophila str. Philadelphia 1 NC_002942 1 0 the initial event of Legionellosis isolate from the initial event of Legionellosis in Philadelphia and is the type strain for this species Clinical/Human-associated 246315 Legionella pneumophila subsp. pneumophila str. Thunder Bay NC_021350.1 1 0 38 year old male isolated from a 38 year old male in Northern Ontario, Canada Clinical/Human-associated 310483 Leifsonia xyli subsp. cynodontis DSM 46306 NC_022438.1 1 0 Plant/agriculture-associated 11655 Leifsonia xyli subsp. xyli str. CTCB07 NC_006087 1 0 Plant/agriculture-associated 188239 Leisingera methylohalidivorans DSM 14336 NC_023135.1,NC_023146.1,NC_023136.1 1 2 seawater collected from a tide pool isolated from rearings and collectors of the scallop Pecten maximus (in Galicia, Spain), and M. algicola, which was isolated from a stationary culture of the toxin-producing marine dinoflagellate Prorocentrum lima (in Vigo, Spain) Aquatic-environment 112363 Leptolyngbya sp. PCC 7376 NC_019683.1 1 0 Crystal Cave (limestone) Extreme-environment 95142 Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)' NC_010842,NC_010845,NC_010846 2 1 stream water Aquatic-environment 123590 Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' NC_010602,NC_010843,NC_010844 2 1 Aquatic-environment 13265 Leptospira borgpetersenii serovar Hardjo-bovis JB197 NC_008510,NC_008511 2 0 Strain JB197 was isolated in the U.S. from a beef steer at slaughter Terrestrial-animal-associated 75619 Leptospira borgpetersenii serovar Hardjo-bovis L550 NC_008508,NC_008509 2 0 human Clinical/Human-associated sample, strain L550 was isolated in Australia from a human patient with leptospirosis contracted from exposure to infected cattle isolated from a human Clinical/Human-associated sample and will be used for comparative genomics with other Leptospira species Clinical/Human-associated 6257 Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 NC_005823,NC_005824 2 0 patient with severe leptospirosis during an epidemic isolated from a patient with severe leptospirosis during an epidemic in 1996 Clinical/Human-associated 91350 Leptospira interrogans serovar Lai str. 56601 NC_004342,NC_004343 2 0 Clinical/Human-associated 111724 Leptospira interrogans serovar Lai str. IPAV NC_017551,NC_017552 2 0 high passage avirulent strain derived by prolonged laboratory passage from a highly virulent ancestral strain isolated in China Lab/Engineered 240525 Leptospirillum ferriphilum ML-04 NC_018649 1 0 "isolated from acidic water near a hot spring in Tengchong, Yunnan province of China" Extreme-environment 235441 Leptospirillum ferrooxidans C2-3 NC_017094.1 1 0 fresh volcanic ash deposit isolated from fresh volcanic ash deposit in the island of Miyake, Japan Extreme-environment 83238 Leptothrix cholodnii SP-6 NC_010524 1 0 water and flocculent from an artificial iron seep isolated from water and flocculent from an artificial iron seep in Ithaca, NY Polluted/impacted environment 70646 Leptotrichia buccalis C-1013-b NC_013192 1 0 dental plaque isolated from dental plaque Clinical/Human-associated 254563 Leuconostoc carnosum JB16 NC_018673.1,NC_018675.1,NC_018674.1,NC_018699.1,NC_018698.1 1 4 Isolated from Kimchi Food-associated 37309 Leuconostoc citreum KM20 NC_010471,NC_010467,NC_010469,NC_010470,NC_010466 1 4 Baechu kimchi Food-associated 160647 Leuconostoc gasicomitatum LMG 18811 NC_014319 1 0 Modified-atmosphere packaged, tomato-marinated broiler meat strips; Finland Food-associated 256080 Leuconostoc gelidum JB7 NC_018631.1 1 0 Kimchi, traditional fermented food Food-associated 161478 Leuconostoc kimchii IMSNU 11154 NC_014136,NC_014131,NC_014135,NC_014132,NC_014133,NC_014134 1 5 ermented kimchi in Korea Food-associated 50664 Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 NC_008531,NC_008496 1 1 fermenting olives Food-associated 214937 Leuconostoc mesenteroides subsp. mesenteroides J18 NC_016805,NC_016827,NC_016820,NC_016821,NC_016828,NC_016806 1 5 Isolated from baechu (Chinese cabbage) kimchi fermented at 4 deg C. Food-associated 185776 Leuconostoc sp. C2 NC_015734 1 0 Food-associated 253119 Liberibacter crescens BT-1 NC_019907.1 1 0 mountain papaya Plant/agriculture-associated 102668 Listeria innocua Clip11262 NC_003212,NC_003383 1 1 dairy products (cheese) from Morocco Food-associated 209121 Listeria ivanovii NC_016011 1 0 infected ewe isolated from an infected ewe and has a lower virulence than the type strain Terrestrial-animal-associated 240031 Listeria monocytogenes 07PF0776 NC_017728.1 1 0 Clinical/Human-associated 5116 Listeria monocytogenes 08-5923 NC_013768 1 0 Human, canada Clinical/Human-associated Listeria monocytogenes 10403S NC_017544 1 0 mice streptomycin resistant isolate of strain 10403 Terrestrial-animal-associated 159512 Listeria monocytogenes 8-5578 NC_013766,NC_013767 1 1 human Clinical/Human-associated 174445 Listeria monocytogenes ATCC 19117 NC_018584.1 1 0 Sheep Terrestrial-animal-associated Listeria monocytogenes EGD NC_022568 1 0 rabbit tissue Terrestrial-animal-associated 69206 Listeria monocytogenes EGD-e NC_003210 1 0 the strain EGD derived from the strain EGD that was used in studies of cell-mediated immunity, Rabbit (UK) Terrestrial-animal-associated Listeria monocytogenes Finland 1998 NC_017547 1 0 food-borne pathogen food-associated Listeria monocytogenes FSL R2-561 NC_017546 1 0 food-associated 86872 Listeria monocytogenes HCC23 NC_011660 1 0 channel catfish isolated from channel catfish Aquatic-life-associated Listeria monocytogenes J016 NC_017545 1 0 A deli in the United States in 2000 during an epidemic outbreak food-associated Listeria monocytogenes J1-220 NC_021830 1 0 J1-220, involved in an outbreak associated with vegetables. food-associated Listeria monocytogenes J1776 NC_021839,NC_022046 1 1 Food-associated Listeria monocytogenes J1816 NC_021829 1 0 involved in the 2002 U.S. outbreak associated with turkey deli meat food-associated Listeria monocytogenes J1926 NC_021840,NC_022051 1 1 food-associated Listeria monocytogenes J2-031 NC_021837 1 0 Food-associated Listeria monocytogenes J2-064 NC_021824 1 0 Food-associated Listeria monocytogenes J2-1091 NC_021825 1 0 Food-associated 258987 Listeria monocytogenes L312 NC_018642.1 1 0 Cheese Food-associated 120152 Listeria monocytogenes La111 NC_020557.1 1 0 two different Danish fish processers isolated six years apart from two different Danish fish processers Polluted/impacted environment 196182 Listeria monocytogenes M7 NC_017537 1 0 cows milk Terrestrial-animal-associated Listeria monocytogenes N1-011A NC_021826,NC_022045 1 1 Food-associated 260307 Listeria monocytogenes N53-1 NC_020558.1 1 0 two different Danish fish processers isolated six years apart from two different Danish fish processers Polluted/impacted environment Listeria monocytogenes R2-502 NC_021838,NC_021828 1 1 responsible for a gastrointestinal listeriosis outbreak in the US in 1994 Food-associated 177243 Listeria monocytogenes serotype 1/2b str. SLCC2755 NC_018587.1,NC_014495.1 1 1 chinchilla Terrestrial-animal-associated 180744 Listeria monocytogenes serotype 1/2c str. SLCC2372 NC_018588.1,NC_018889 1 1 Human, UK Clinical/Human-associated 174077 Listeria monocytogenes serotype 4a str. L99 NC_017529 1 0 Originally isolated from contaminated food by Kampelmacher in 1950s in the Netherlands. Cheese, Netherlands Food-associated 88360 Listeria monocytogenes serotype 4b str. CLIP 80459 NC_012488 1 0 unknown 105049 Listeria monocytogenes serotype 4b str. F2365 NC_002973 1 0 isolated in 1985 in California, USA, during an outbreak of listeriosis among patients with AIDS Clinical/Human-associated 265196 Listeria monocytogenes serotype 4b str. LL195 NC_019556.1 1 0 isolated from Swiss Listeriosis epidemic Clinical/Human-associated 174802 Listeria monocytogenes serotype 7 str. SLCC2482 NC_018591.1 1 0 human 1966 Clinical/Human-associated 171973 Listeria monocytogenes SLCC2376 NC_018590.1 1 0 Poultry Terrestrial-animal-associated 169669 Listeria monocytogenes SLCC2378 NC_018585.1 1 0 poultry Terrestrial-animal-associated 253052 Listeria monocytogenes SLCC2479 NC_018589.1 1 0 unknown 174253 Listeria monocytogenes SLCC2540 NC_018586.1 1 0 Human, USA Clinical/Human-associated 253068 Listeria monocytogenes SLCC5850 NC_018592.1 1 0 Rabbit, UK Terrestrial-animal-associated 172295 Listeria monocytogenes SLCC7179 NC_018593.1 1 0 cheese, Austria Food-associated Listeria monocytogenes strain C1-387 NC_021823 1 0 Food-associated Listeria monocytogenes strain J1817 NC_021827,NC_022047 1 1 2002 U.S. outbreak associated with turkey deli meat food-associated 138575 Listeria seeligeri serovar 1/2b str. SLCC3954 NC_013891 1 0 Soil soil 39304 Listeria welshimeri serovar 6b str. SLCC5334 NC_008555 1 0 decaying plant material Plant/agriculture-associated 173599 Listonella anguillarum M3 NC_022223.1,NC_022224.1,NC_022225.1 2 1 flounder (Paralichthys olivaceous), is presented isolated from flounder (Paralichthys olivaceous), is presented Terrestrial-animal-associated 89750 Lysinibacillus sphaericus C3-41 NC_010382,NC_010381 1 1 mosquito breeding site isolated from a mosquito breeding site in China Insect-associated/other symbiont 48391 Macrococcus caseolyticus JCSC5402 NC_011999,NC_011996,NC_011995,NC_011997,NC_011998,NC_012000,NC_012001,NC_012002,NC_012003 1 8 animal meat isolated from animal meat in a supermarket Food-associated 23654 Magnetococcus sp. MC-1 NC_008576 1 0 water from the Pettaquamscutt Estuary, isolated from water from the Pettaquamscutt Estuary, in Rhode Island, USA Aquatic-environment 129836 Magnetospirillum magneticum AMB-1 NC_007626 1 0 Pond water in Tokyo Japan Aquatic-environment 157719 Mahella australiensis 50-1 BON NC_015520 1 0 Riverslea oil field in the Bowen-Surat basin, Australia Extreme-environment 278710 Mannheimia haemolytica D153 NC_021743.1 1 0 feedlot; body_site: lung; sample_type: lung specimen Terrestrial-animal-associated 280723 Mannheimia haemolytica D171 NC_021738.1 1 0 pneumonic lung specimen from feedlot steer Terrestrial-animal-associated 283117 Mannheimia haemolytica D174 NC_021739.1 1 0 pneumonic lung specimen from feedlot steer Terrestrial-animal-associated 297097 Mannheimia haemolytica M42548 NC_021082.1 1 0 upper respiratory tract and nasopharynx upper respiratory tract and nasopharynx Terrestrial-animal-associated 283577 Mannheimia haemolytica USDA-ARS-USMARC-183 NC_020833.1 1 0 Terrestrial-animal-associated 283342 Mannheimia haemolytica USDA-ARS-USMARC-185 NC_020834.1 1 0 mucus Terrestrial-animal-associated 299788 Mannheimia haemolytica USMARC_2286 NC_021883.1 1 0 Terrestrial-animal-associated 86752 Mannheimia succiniciproducens MBEL55E NC_006300 1 0 bovine rumen isolated from a bovine rumen and will provide information on the protiens involved in succinc acid production Terrestrial-animal-associated 16383 Maribacter sp. HTCC2170 NC_014472 1 0 coastal area of Newport, Oregon at a depth of 10 meters collected from the coastal area of Newport, Oregon at a depth of 10 meters and was isolated by plating on solid media. Aquatic-environment 77530 Maricaulis maris MCS10 NC_008347 1 0 Puget Sound isolated from Puget Sound in Washington and will be used for comparative analysis Aquatic-environment 166763 Marinithermus hydrothermalis DSM 14884 NC_015387 1 0 eep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1,385 m Extreme-environment 40839 Marinitoga piezophila KA3 NC_016748,NC_016751 1 1 deep-sea hydrothermal vent chimney at a depth of 2630 meters on the East-Pacific Rise Extreme-environment 104501 Marinobacter adhaerens HP15 NC_017506,NC_017507,NC_017508 1 2 isolated from marine particles sampled in the German Wadden Sea Aquatic-environment 65105 Marinobacter aquaeolei VT8 NC_008740,NC_008739,NC_008738 1 2 oil well off the coast of Vietnam isolated from an oil well off the coast of Vietnam Extreme-environment 236848 Marinobacter hydrocarbonoclasticus ATCC 49840 NC_017067.1 1 0 polluted seawater and sediments near a petroleum refinery, Gulf of Fos, Mediterranean coast of France Polluted/impacted environment 97766 Marinobacter sp. BSs20148 NC_018268.1 1 0 isolated from marine sediment collected from the Arctic Ocean at a water depth of 3,800 m Aquatic-environment 159599 Marinomonas mediterranea MMB-1 NC_015276 1 0 Mediterranean seawater from the southeastern coast of Spain, 1995 Aquatic-environment 2975 Marinomonas posidonica IVIA-Po-181 NC_015559 1 0 seagrass Posidonia oceanica in different meadows in the coast of the 76 Balearic Islands (Spain) Plant/agriculture-associated 124341 Marinomonas sp. MWYL1 NC_009654 1 0 Isolated from root surface of the salt marsh grass Spartina anglica, near the North Norfolk (England) village of Stiffkey Plant/agriculture-associated 126157 Marivirga tractuosa DSM 4126 NC_014759,NC_014750 1 1 beach sand from Nha Trang Aquatic-environment 147215 Megamonas hypermegale ART12/1 NC_021041 1 0 Clinical/Human-associated 207727 Megasphaera elsdenii DSM 20460 NC_015873 1 0 Rumen of sheep Terrestrial-animal-associated 128672 Meiothermus ruber DSM 1279 NC_013946 1 0 hot spring isolated from a hot spring Extreme-environment 18825 Meiothermus silvanus DSM 9946 NC_014212,NC_014213,NC_014214 1 2 hot spring isolated from a hot spring in Portugal Extreme-environment 241275 Melioribacter roseus P3M NC_018178.1 1 0 microbial mat, developing on the wooden surface of a chute, under the flow of hot water coming from an oil exploring well Extreme-environment 182073 Melissococcus plutonius ATCC 35311 NC_015516,NC_015517 1 1 insect (honey bee larvae) Insect-associated/other symbiont 217605 Melissococcus plutonius DAT561 NC_016938.1,NC_018265.1 1 1 isolated from diseased honeybees larvae with clinical signs of EFB in Japan Insect-associated/other symbiont 3168 Mesoplasma florum L1 NC_006055 1 0 the surface of the lemon tree flower isolated from the surface of the lemon tree flower Plant/agriculture-associated 315161 Mesoplasma florum W37 NC_022583.1 1 0 Solidago sp Isolated from a Solidago sp Plant/agriculture-associated 160642 Mesorhizobium ciceri biovar biserrulae WSM1271 NC_014923,NC_014918 1 1 root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin Plant/agriculture-associated 2464 Mesorhizobium loti MAFF303099 NC_002678,NC_002679,NC_002682 1 2 Japanese bird's-foot trefoil Plant/agriculture-associated 111569 Methylacidiphilum infernorum V4 NC_010794 1 0 isolated from the Hell's Gate geothermal area in New Zealand Extreme-environment 12200 Methylibium petroleiphilum PM1 NC_008825,NC_008826 1 1 the biofilter of a treatment plant isolated in 1998 from the biofilter of a treatment plant in an oil refinery in Los Angeles, California Polluted/impacted environment 97085 Methylobacillus flagellatus KT NC_007947 1 0 activated sludge found at the wastewater treatment plant isolated from activated sludge found at the wastewater treatment plant in Moscow, Russia and is the fastest growing methylotroph discovered Polluted/impacted environment 132133 Methylobacterium chloromethanicum CM4 NC_011757,NC_011760,NC_011758 1 2 Soil at a petrochemical factory in Tatarstan Russia Polluted/impacted environment 101010 Methylobacterium extorquens AM1 NC_012808,NC_012807,NC_012809,NC_012810,NC_012811 1 4 First isolated in 1960 in Oxford, England, as an airborne contaminant growing on methylamine. unknown 143287 Methylobacterium extorquens DM4 NC_012988,NC_012989,NC_012987 1 2 soil contaminated with halogenated (chlorine-containing) hydrocarbons isolated from soil contaminated with halogenated (chlorine-containing) hydrocarbons Polluted/impacted environment 98426 Methylobacterium extorquens PA1 NC_010172 1 0 Plant/agriculture-associated 76414 Methylobacterium nodulans ORS 2060 NC_011894,NC_011887,NC_011893,NC_011895,NC_011888,NC_011889,NC_011890,NC_011892 1 7 Root nodules from the legume Crotalaria Plant/agriculture-associated 124700 Methylobacterium populi BJ001 NC_010725,NC_010721,NC_010727 1 2 poplar plantlets and from tissue cultures (Populus deltoidesxnigra DN34) that were developed initially from surface-sterilized explants and maintained under axenic conditions Plant/agriculture-associated 70578 Methylobacterium radiotolerans JCM 2831 NC_010505,NC_010509,NC_010510,NC_010514,NC_010502,NC_010504,NC_010517,NC_010518,NC_010507 1 8 unpolished rice Plant/agriculture-associated 32184 Methylobacterium sp. 4-46 NC_010511,NC_010374,NC_010373 1 2 Nodulates Lotononis bainesii and a photosynthesizer, unlike other Methylobacterium strains or any of their close relatives Plant/agriculture-associated 55537 Methylocella silvestris BL2 NC_011666 1 0 isolated from an acidic forest soil Extreme-environment 22254 Methylococcus capsulatus str. Bath NC_002977 1 0 purchased from National Collection of Industrial and Marine Bacteria unknown 20402 Methylocystis sp. SC2 NC_018485.1 1 0 highly polluted aquifer isolated from a highly polluted aquifer in Germany Polluted/impacted environment 68050 Methylomicrobium alcaliphilum NC_016112 1 0 Extreme-environment 172210 Methylomonas methanica MC09 NC_015572 1 0 coastal seawater waters obtained from the Bristol Channel just outside of Penarth in the UK which is a large estuary leading to the Irish Sea. Aquatic-environment 147481 Methylophaga sp. JAM1 NC_017857.1 1 0 isolated from a methanol-fed denitrification system treating seawater at the Montreal Biodome Polluted/impacted environment 147316 Methylophaga sp. JAM7 NC_017856.1,NC_017858.1 1 1 isolated from a methanol-fed denitrification system treating seawater at the Montreal Biodome Polluted/impacted environment 89187 Methylotenera mobilis JLW8 NC_012968 1 0 Isolated from Lake Washington in Seattle, Washington, USA. Aquatic-environment 140979 Methylotenera versatilis 301 NC_014207 1 0 Lake Washington sediment Aquatic-environment 170262 Methylovorus sp. MP688 NC_014733 1 0 soil isolated from soil and produces pyrroloquinoline quinone which has potential pharmaceutical applications soil 110381 Methylovorus sp. SIP3-4 NC_012969,NC_012970,NC_012972 1 2 Lake Washington sediment Aquatic-environment 161757 Micavibrio aeruginosavorus ARL-13 NC_016026 1 0 sewage water sewage water Polluted/impacted environment 134007 Micavibrio aeruginosavorus EPB NC_020812 1 0 unknown 185510 Microbacterium testaceum StLB037 NC_015125 1 0 isolated from potato leaves Plant/agriculture-associated 29563 Micrococcus luteus NCTC 2665 NC_012803 1 0 Originally isolated by Alexander Fleming in 1929 as Micrococcus lysodeikticus Lab/Engineered 236384 Microcoleus sp. PCC 7113 NC_019738.1,NC_019742.1,NC_019761.1,NC_019739.1,NC_019760.1,NC_019762.1,NC_019743.1,NC_019741.1,NC_019740.1 1 8 Soil, orchid house isolated from Soil, orchid house, San Francisco, USA soil 59304 Microcystis aeruginosa NIES-843 NC_010296 1 0 Lake Kasumigaura Ibaraki Japan from Otsuka, Shigeto Aquatic-environment 197753 Microlunatus phosphovorus NM-1 NC_015635 1 0 Activated sludge Polluted/impacted environment 74833 Micromonospora aurantiaca ATCC 27029 NC_014391 1 0 soil isolated from soil soil 154089 Micromonospora sp. L5 NC_014815 1 0 roots of the Casuarina equisetifolia isolated from the roots of the Casuarina equisetifolia in Irapuato, Mexico Plant/agriculture-associated 30313 Mobiluncus curtisii ATCC 43063 NC_014246 1 0 Clinical/Human-associated 128783 Modestobacter marinus BC501 NC_017955.1 1 0 isolated from a white marble surface in Carrara, Tuscany, Italy soil 6753 Moorella thermoacetica ATCC 39073 NC_007644 1 0 Bottom of stagnant ponds Aquatic-environment 148474 Moraxella catarrhalis RH4 NC_014147 1 0 human blood isolated from human blood and will be used for comparative analysis Clinical/Human-associated Morganella morganii subsp. morganii KT NC_020418 1 0 Isolated from blood during postoperative care of 57-year-old male cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia at Changhua Christian Hospital, Taiwan. Clinical/Human-associated 171000 Muricauda ruestringensis DSM 13258 NC_015945 1 0 Seawater sediment suspension containing hexadecane; Germany, North Sea coast. Polluted/impacted environment 55940 Mycobacterium abscessus ATCC 19977 NC_010397,NC_010394 1 1 Originally isolated from a human knee infection with subcutaneous abscess-like lesions in 1953. Clinical/Human-associated 291813 Mycobacterium abscessus subsp. bolletii 50594 NC_021282.1,NC_021279.1,NC_021278.1 1 2 patient with a pulmonary infection Clinical/Human-associated 123451 Mycobacterium africanum GM041182 NC_015758 1 0 isolated in The Gambia in 2004 from a 27 year old HIV uninfected male patient Clinical/Human-associated 38287 Mycobacterium avium 104 NC_008595 1 0 AIDS patient and has been characterized for virulence derived from an AIDS patient and has been characterized for virulence in the murine model of low-dose aerosol infection in that it could colonize the lung, proliferate within the tissue and disseminate to other organs Clinical/Human-associated 108102 Mycobacterium avium subsp. paratuberculosis K-10 NC_002944 1 0 Bovine Johne's disease isolated from a dairy herd in Wisconsin in the 1970's by investigators from the USDA National Animal Disease Center Terrestrial-animal-associated 245745 Mycobacterium avium subsp. paratuberculosis MAP4 NC_021200.1 1 0 humans and those associated with bovine Johne¿¿¿¿¿¿¿s disease, we characterized the complete genome sequence of strain MAP4 recovered from the breast milk of a Crohn¿¿¿¿¿¿¿s disease patient recovered from humans and those associated with bovine Johne¿¿¿¿¿¿¿s disease, we characterized the complete genome sequence of strain MAP4 recovered from the breast milk of a Crohn¿¿¿¿¿¿¿s disease patient Clinical/Human-associated 88188 Mycobacterium bovis AF2122/97 NC_002945 1 0 cow suffering necrotic lesions isolated in 1997 in the UK from a cow suffering necrotic lesions in lung and bronchomediastinal lymph nodes Terrestrial-animal-associated 250740 Mycobacterium bovis BCG str. Korea 1168P NC_020245.2 1 0 derived from an M. bovis strain isolated after 230 serial passages on glycerol-potato-bile medium from 1908 to 1921 by Albert Calmette and Camille Guérin at the Institut Pasteur in Lille, France Lab/Engineered 159397 Mycobacterium bovis BCG str. Mexico NC_016804 1 0 used to create vaccine Lab/Engineered 80988 Mycobacterium bovis BCG str. Pasteur 1173P2 NC_008769 1 0 vaccine related Lab/Engineered 85238 Mycobacterium bovis BCG str. Tokyo 172 NC_012207 1 0 used for tuberculosis vaccine Lab/Engineered 203588 Mycobacterium canettii CIPT 140010059 NC_015848 1 0 Clinical/Human-associated 278382 Mycobacterium canettii CIPT 140060008 NC_019950.1 1 0 Pulmonary human Clinical/Human-associated isolates Clinical/Human-associated 273172 Mycobacterium canettii CIPT 140070008 NC_019965.1 1 0 Lymph node human Clinical/Human-associated isolates Clinical/Human-associated 270121 Mycobacterium canettii CIPT 140070010 NC_019951.1 1 0 Skin human Clinical/Human-associated isolates Clinical/Human-associated 265803 Mycobacterium canettii CIPT 140070017 NC_019952.1 1 0 Lymph node human Clinical/Human-associated isolates Clinical/Human-associated 153207 Mycobacterium chubuense NBB4 NC_018027.1,NC_018023.1,NC_018022.1 1 2 Estuarine Sediment soils and sediments from the Sydney region (New South Wales, Australia) Aquatic-environment 17082 Mycobacterium gilvum PYR-GCK NC_009338,NC_009340,NC_009341,NC_009339 1 3 river sediment isolated from river sediment and will be used for comparative genomics Aquatic-environment Mycobacterium gilvum Spyr1 NC_014814,NC_014811,NC_014812 1 2 Isolated from Perivleptos, a creosote polluted site in Epirus, Greece (12 Km North of the city of Ioannina), where a wood preserving industry was operating for over 30 years. Polluted/impacted environment 261808 Mycobacterium indicus pranii MTCC 9506 NC_018612.1 1 0 Lab/Engineered Mycobacterium intracellulare ATCC 13950 NC_016946 1 0 unknown 226976 Mycobacterium intracellulare MOTT-02 NC_016947.1 1 0 Korean patients Clinical/Human-associated 229198 Mycobacterium intracellulare MOTT-64 NC_016948.1 1 0 Clinical/Human-associated Mycobacterium kansasii ATCC 12478 NC_022663,NC_022654 1 0 Clinical/Human-associated 121698 Mycobacterium leprae Br4923 NC_011896 1 0 human skin biopsy isolated from a human skin biopsy in Brazil, and passaged in nude mice and armadillos Clinical/Human-associated 78757 Mycobacterium leprae TN NC_002677 1 0 This strain (TN) was passaged through an armadillo in Tamil Nadu, India Terrestrial-animal-associated Mycobacterium liflandii 128FXT NC_020133,NC_011355 1 1 Originally isolated from infected Xenopus tropicalis at the University of California, Berkeley. frog Terrestrial-animal-associated 75906 Mycobacterium marinum M NC_010612,NC_010604 1 1 human Clinical/Human-associated 249549 Mycobacterium massiliense str. GO 06 NC_018150.1 1 0 wound samples of patients submitted to arthroscopic and laparoscopic surgeries had its genome sequenced recovered from wound samples of patients submitted to arthroscopic and laparoscopic surgeries had its genome sequenced Clinical/Human-associated Mycobacterium neoaurum VKM Ac-1815D NC_023036 1 0 originally isolated from soil samples Soil 150181 Mycobacterium rhodesiae NBB3 NC_016604 1 0 Estuarine Sediment soils and sediments from the Sydney region (New South Wales, Australia) Aquatic-environment 175119 Mycobacterium smegmatis JS623 NC_019966.1,NC_019959.1,NC_019958.1,NC_019957.1 1 3 Soil derived from sandy garden soil (Panama City, Fla.) soil Mycobacterium smegmatis MC2 155 NC_018289 1 0 Lab/engineered 59918 Mycobacterium smegmatis str. MC2 155 NC_008596 1 0 Mutant of M smegmatis isolated on 1990 isolated in 1990 Lab/Engineered 168628 Mycobacterium sp. JDM601 NC_015576 1 0 patient with tubersulosis-like disease and with high resistance to various antibiotics Clinical/Human-associated 51234 Mycobacterium sp. JLS NC_009077 1 0 creosote-contaminated soil from the Champion International Superfund site isolated from creosote-contaminated soil from the Champion International Superfund site in Libby, Montana Polluted/impacted environment 70743 Mycobacterium sp. KMS NC_008705,NC_008704,NC_008703 1 2 creosote-contaminated soil from the Champion International Superfund site isolated from creosote-contaminated soil from the Champion International Superfund site in Libby, Montana Polluted/impacted environment 106721 Mycobacterium sp. MCS NC_008146,NC_008147 1 1 Creosote-contaminated soil from the Champion International Superfund site in Libby Montana Polluted/impacted environment 238734 Mycobacterium sp. MOTT36Y NC_017904.1 1 0 Korean patient isolated Mycobacterium sp Clinical/Human-associated 272950 Mycobacterium tuberculosis 7199-99 NC_020089 1 0 Clinical/Human-associated 287820 Mycobacterium tuberculosis CAS/NITR204 NC_021193.1 1 0 Tamilnadu, India was performed using paired read sequencing on Illumina Hiseq 2000 isolate from Tamilnadu, India was performed using paired read sequencing on Illumina Hiseq 2000 Clinical/Human-associated 49375 Mycobacterium tuberculosis CCDC5079 NC_017523 1 0 Collected from patients with secondary pulmonary tuberculosis at a hospital in Fujian Province, China, in 2004. Clinical/Human-associated Mycobacterium tuberculosis CCDC5079 NC_021251 1 0 Clinical/Human-associated 59413 Mycobacterium tuberculosis CCDC5180 NC_017522 1 0 patient with secondary pulmonary tuberculosis isolated in 2004 from a patient with secondary pulmonary tuberculosis Clinical/Human-associated 22151 Mycobacterium tuberculosis CDC1551 NC_002755 1 0 clothing factory worker from the Kentucky/Tennessee, USA, region isolate from a clothing factory worker from the Kentucky/Tennessee, USA, region Clinical/Human-associated 149592 Mycobacterium tuberculosis CTRI-2 NC_017524 1 0 isolated in Russia belongs to AI family (according to RFLP genotyping) Clinical/Human-associated 281501 Mycobacterium tuberculosis EAI5 NC_021740.1 1 0 Mumbai was isolated and whole genome was sequenced using Illumina Sequencing is from Mumbai was isolated and whole genome was sequenced using Illumina Sequencing Clinical/Human-associated 279388 Mycobacterium tuberculosis EAI5/NITR206 NC_021194.1 1 0 Tamilnadu, India was performed using paired read sequencing on Illumina Hiseq 2000 isolate from Tamilnadu, India was performed using paired read sequencing on Illumina Hiseq 2000 Clinical/Human-associated Mycobacterium tuberculosis Erdman = ATCC 35801 NC_020559 1 0 Isolated from human sputum at Mayo Clinic, Rochester, Minnesota. Clinical/Human-associated 9078 Mycobacterium tuberculosis F11 NC_009565 1 0 tuberculosis patients during a TB epidemic recovered from tuberculosis patients during a TB epidemic in the Western Cape of South Africa Clinical/Human-associated 106795 Mycobacterium tuberculosis H37Ra NC_009525 1 0 avirulent strain derived from its virulentparent strain H37 derived from its virulentparent strain H37 (isolated from a 19 year-old male patient with chronic pulmonary tuberculosis by Edward R. Baldwin in 1905) through a process of aging and dissociation from in vitro culture in 1935 Clinical/Human-associated 87468 Mycobacterium tuberculosis H37Rv NC_000962 1 0 derived from the original human-lung H37 isolate derived from the original human-lung H37 isolate in 1934, and has been used extensively worldwide in biomedical research Clinical/Human-associated 226894 Mycobacterium tuberculosis H37Rv (Broad) NC_000962 1 0 Isolated from human lung in 1905 and passaged outside of the human host. Clinical/Human-associated 169848 Mycobacterium tuberculosis H37RvAE NC_018143 1 0 unknown Mycobacterium tuberculosis Haarlem NC_022350 1 0 isolated from Harleem, Netherlands Clinical/Human-associated 122270 Mycobacterium tuberculosis KZN 1435 NC_012943 1 0 patient isolated from a patient in KwaZulu-Natal, South Africa Clinical/Human-associated 226895 Mycobacterium tuberculosis KZN 4207 (Broad) NC_016768 1 0 Patient in KwaZulu-Natal, South Africa Clinical/Human-associated Mycobacterium tuberculosis KZN 605 NC_018078 1 0 patients from KwaZulu-Natal region clinical/Human-associated 234965 Mycobacterium tuberculosis RGTB327 NC_017026.1 1 0 isolated from sputum samples of patients Clinical/Human-associated isolates of Mycobacterium tuberculosis isolated from Kerala, India. Clinical/Human-associated 229356 Mycobacterium tuberculosis RGTB423 NC_017528.1 1 0 isolated from sputum samples of patients Clinical/Human-associated isolates of Mycobacterium tuberculosis isolated from Kerala, India. Clinical/Human-associated 279038 Mycobacterium tuberculosis str. Beijing/NITR203 NC_021054.1 1 0 Tamilnadu, India was performed using paired read sequencing on Illumina Hiseq 2000 isolate from Tamilnadu, India was performed using paired read sequencing on Illumina Hiseq 2000 Clinical/Human-associated 282484 Mycobacterium tuberculosis str. Haarlem/NITR202 NC_021192.1 1 0 Tamilnadu, India was performed using paired read sequencing on Illumina Hiseq 2000 isolate from Tamilnadu, India was performed using paired read sequencing on Illumina Hiseq 2000 Clinical/Human-associated 227229 Mycobacterium tuberculosis UT205 NC_016934 1 0 Isolated from sputum of a 33-year-old man with recently diagnosed tuberculosis. Sputum of a tuberculosis patient, Medell?n, Antioquia, Colombia. Clinical/Human-associated 37413 Mycobacterium ulcerans Agy99 NC_008611,NC_005916 1 1 ulcerative lesion on the right elbow of a female patient from the Ga district of Ghana in 1999 Clinical/Human-associated 31953 Mycobacterium vanbaalenii PYR-1 NC_008726 1 0 contaminated sites exposed to petrogenic chemicals isolated from contaminated sites exposed to petrogenic chemicals in the watershed of Redfish Bay, Texas, in 1986 Polluted/impacted environment 233134 Mycobacterium yongonense 05-1390 NC_021715.1,NC_020275.1,NC_020276.1 1 2 pulmonary patient Clinical/Human-associated 82602 Mycoplasma agalactiae 5632 NC_013948.1 1 0 Goat in Spain Terrestrial-animal-associated 119067 Mycoplasma agalactiae PG2 NC_009497 1 0 Goat in Spain Terrestrial-animal-associated 31993 Mycoplasma arthritidis 158L3-1 NC_011025 1 0 MAV1 lysogen strain 158L3-1 of the parent strain 158. Lab/Engineered 163258 Mycoplasma bovis HB0801 NC_018077.1 1 0 the lung of an infected cattle from the farm isolated from the lung of an infected cattle from the farm in the city of Yingcheng in Hubei province, China Terrestrial-animal-associated 183966 Mycoplasma bovis Hubei-1 NC_015725 1 0 isolated in 2008 that caused calf pneumonia on a Chinese farm Terrestrial-animal-associated 114686 Mycoplasma bovis PG45 NC_014760 1 0 bovine mastitis Terrestrial-animal-associated 130493 Mycoplasma capricolum subsp. capricolum ATCC 27343 NC_007633 1 0 caprine (Goat) Terrestrial-animal-associated 56923 Mycoplasma conjunctivae HRC/581 NC_012806 1 0 sheep and goats in naturally occurring outbreaks of keratoconjunctivitis (pink-eye) Terrestrial-animal-associated 43672 Mycoplasma crocodyli MP145 NC_014014 1 0 joint of a crocodile with exudative polyarthritis Terrestrial-animal-associated 277645 Mycoplasma cynos C142 NC_019949.1 1 0 dog with canine infectious respiratory disease (CIRD) isolated from a dog with canine infectious respiratory disease (CIRD) in the USA Terrestrial-animal-associated 34481 Mycoplasma fermentans JER NC_014552 1 0 Respiratory and urogenital tract of immunocompromised humans Clinical/Human-associated 179416 Mycoplasma fermentans M64 NC_014921 1 0 a non-AIDS patient with acute respiratory disease Clinical/Human-associated 131377 Mycoplasma fermentans PG18 NC_021002 1 0 genital ulcer isolated from a genital ulcer and will be used for comparative analysis Clinical/Human-associated 251791 Mycoplasma gallisepticum CA06_2006.052-5-2P NC_018412.1 1 0 House finch-associated HFMG house finches in different years and different states Terrestrial-animal-associated 237080 Mycoplasma gallisepticum NC06_2006.080-5-2P NC_018411.1 1 0 house finches in different years and different states Terrestrial-animal-associated 255949 Mycoplasma gallisepticum NC08_2008.031-4-3P NC_018413.1 1 0 house finches in different years and different states Terrestrial-animal-associated 238389 Mycoplasma gallisepticum NC95_13295-2-2P NC_018407.1 1 0 house finches in different years and different states Terrestrial-animal-associated 257564 Mycoplasma gallisepticum NC96_1596-4-2P NC_018408.1 1 0 Terrestrial-animal-associated 236098 Mycoplasma gallisepticum NY01_2001.047-5-1P NC_018409.1 1 0 house finches in different years and different states Terrestrial-animal-associated 151358 Mycoplasma gallisepticum str. F NC_017503 1 0 12-Year Epizootic in House Finche populations starting in Washington, D. C. in 1994 Terrestrial-animal-associated 149415 Mycoplasma gallisepticum str. R(high) NC_017502 1 0 Clonal isolate Lab/Engineered 115357 Mycoplasma gallisepticum str. R(low) NC_004829 1 0 Clonal isolate Lab/Engineered 233754 Mycoplasma gallisepticum VA94_7994-1-7P NC_018406.1 1 0 house finches in different years and different states Terrestrial-animal-associated 229072 Mycoplasma gallisepticum WI01_2001.043-13-2P NC_018410.1 1 0 house finches in different years and different states Terrestrial-animal-associated 98045 Mycoplasma genitalium G37 NC_000908 1 0 male patient with nongonococcal urethritis isolated as a urethral specimen from a male patient with nongonococcal urethritis Clinical/Human-associated 138043 Mycoplasma genitalium M2288 NC_018498.1 1 0 isolated originally from male with symptomatic urethritis at Copenhagen, Denmark Clinical/Human-associated 140682 Mycoplasma genitalium M2321 NC_018495.1 1 0 isolated originally from male with symptomatic urethritis at Copenhagen, Denmark Clinical/Human-associated 139474 Mycoplasma genitalium M6282 NC_018496.1 1 0 isolated originally from male with symptomatic urethritis at Miyazaki, Japan Clinical/Human-associated 141361 Mycoplasma genitalium M6320 NC_018497.1 1 0 isolated originally from male with symptomatic urethritis in Australia Clinical/Human-associated 219533 Mycoplasma haemocanis str. Illinois NC_016638 1 0 blood of naturally infected dog Terrestrial-animal-associated 179282 Mycoplasma haemofelis str. Langford 1 NC_014970 1 0 blood taken from an experimentally infected specific pathogen free (SPF)-derived cat at a time of high parasitemia Terrestrial-animal-associated 120329 Mycoplasma hominis PG21 ATCC 23114 NC_013511.1 1 0 Human rectal swab Clinical/Human-associated 171631 Mycoplasma hyopneumoniae 168 NC_017509 1 0 isolated from No. 168 Er-hua-nian pig isolated from No. 168 Er-hua-nian pig (Chinese local breed, very sensitive to M. hyopneumoniae) in China Terrestrial-animal-associated 227186 Mycoplasma hyopneumoniae 168-L NC_021283.1 1 0 the virulent parent strain 168 This field strain was gradually attenuated by more than 300 continuous passages through KM2 cell-free medium (a modified Friis medium) and the 380th passage was named strain 168-L Lab/Engineered 77580 Mycoplasma hyopneumoniae 232 NC_006360 1 0 Terrestrial-animal-associated 159439 Mycoplasma hyopneumoniae 7422 NC_021831.1 1 0 isolated from an infected swine in Lindóia do Sul, Santa Catarina, Brazil Terrestrial-animal-associated 9249 Mycoplasma hyopneumoniae 7448 NC_007332 1 0 infected pig isolated from an infected pig in Lindoia do Sul, Santa Catarina, in Brazil Terrestrial-animal-associated 90918 Mycoplasma hyopneumoniae J NC_007295 1 0 agricultural sample isolated from an agricultural sample Plant/agriculture-associated 123619 Mycoplasma hyorhinis DBS 1050 NC_022807.1 1 0 Swiss albino cell culture Lab/Engineered 224386 Mycoplasma hyorhinis GDL-1 NC_016829 1 0 tissue culture isolate Lab/Engineered 165644 Mycoplasma hyorhinis HUB-1 NC_014448 1 0 the respiratory tract of swine isolate from the respiratory tract of swine Terrestrial-animal-associated 178314 Mycoplasma hyorhinis MCLD NC_017519 1 0 the melanoma cell line LB33 mel A1 isolated from the melanoma cell line LB33 mel A1 Lab/Engineered 224431 Mycoplasma hyorhinis SK76 NC_019552.1 1 0 cloned isolate Complete genome of M.hyorhinis Strain SK76. Arthritogenic strain of M.hyorhinis in swine model. Cloned isolate. Lab/Engineered 207080 Mycoplasma leachii 99/014/6 NC_017521 1 0 calf leg joint suffering from arthritis isolated from a calf leg joint suffering from arthritis Terrestrial-animal-associated 173401 Mycoplasma leachii PG50 NC_014751 1 0 Cattle suffering from arthritis and mastitis in Australia Terrestrial-animal-associated 32482 Mycoplasma mobile 163K NC_006908 1 0 the gills of a fresh-water fish, the tench isolated (1984) from the gills of a fresh-water fish, the tench Aquatic-life-associated 166249 Mycoplasma mycoides subsp. capri LC str. 95010 NC_015407,NC_015431 1 1 isolated from a young female goat (alpine breed) with polyarthritis Terrestrial-animal-associated 165667 Mycoplasma mycoides subsp. mycoides SC str. Gladysdale NC_021025 1 0 cattle isolated prior to 1964 from cattle in Australia Terrestrial-animal-associated 4973 Mycoplasma mycoides subsp. mycoides SC str. PG1 NC_005364 1 0 Bovine Terrestrial-animal-associated 314071 Mycoplasma ovis str. Michigan NC_023062.1 1 0 blood Terrestrial-animal-associated 308491 Mycoplasma parvum str. Indiana NC_022575.1 1 0 blood Terrestrial-animal-associated 56664 Mycoplasma penetrans HF-2 NC_004432 1 0 the tracheal aspirate of a previously healthy HIV-negative patient with severe respiratory symptoms caused isolated from the tracheal aspirate of a previously healthy HIV-negative patient with severe respiratory symptoms caused by this infection Clinical/Human-associated 223059 Mycoplasma pneumoniae 309 NC_016807 1 0 Isolated from a pneumonia patient in Hokkaido, Japan in 1998. Clinical/Human-associated 158725 Mycoplasma pneumoniae FH NC_017504 1 0 Isolated by Hayflick from monkey kidney tissue-culture fluids of the FH strain (Eaton Agent Virus) supplied by C. Liu, who recovered this strain in embryonated eggs from a student with atypical pneumonia. Clinical/Human-associated 110 Mycoplasma pneumoniae M129 NC_000912 1 0 patient with atypical pneumonia Clinical/Human-associated isolate from a patient with atypical pneumonia Clinical/Human-associated 271986 Mycoplasma pneumoniae M129-B7 NC_020076 1 0 Homo sapiens Clinical/Human-associated 29704 Mycoplasma pulmonis UAB CTIP NC_002771 1 0 Originally isolated from a mouse with natural respiratory mycoplasmosis. Terrestrial-animal-associated 157434 Mycoplasma putrefaciens KS1 NC_015946 1 0 goat with arthritis isolated from a goat with arthritis Terrestrial-animal-associated 265160 Mycoplasma putrefaciens Mput9231 NC_021083.1 1 0 unknown 154989 Mycoplasma suis KI3806 NC_015153 1 0 blood Isolated from blood of infected pigs. Terrestrial-animal-associated 162453 Mycoplasma suis str. Illinois NC_015155 1 0 blood of an infected pig harvested from blood of an infected pi Terrestrial-animal-associated 118523 Mycoplasma synoviae 53 NC_007294 1 0 broiler breeder isolated from a broiler breeder in the state of Parana in Brazil Terrestrial-animal-associated 242063 Mycoplasma wenyonii str. Massachusetts NC_018149.1 1 0 white blood cells depleted EDTA blood sample of a cow Terrestrial-animal-associated 124704 Myxococcus fulvus HW-1 NC_015711 1 0 seawater isolated from seawater in China Aquatic-environment 278156 Myxococcus stipitatus DSM 14675 NC_020126.1 1 0 obtained from the Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH (DSMZ) unknown 43560 Myxococcus xanthus DK 1622 NC_008095 1 0 unknown 62011 Nakamurella multipartita DSM 44233 NC_013235 1 0 activated sludge isolated from activated sludge and is able in store polysaccharides inside the cell Polluted/impacted environment 92436 Natranaerobius thermophilus JW/NM-WN-LF NC_010718,NC_010724,NC_010715 1 2 sediment of the sunheated Lake Fazda (Wadi An Natrun, Egypt). Solar-heated, alkaline, hypersaline lake of Wadi An Natrun, Egypt Extreme-environment 131435 Nautilia profundicola AmH NC_012115 1 0 epidermis of Alvinella pompejan This strain was isolated from the epidermis of Alvinella pompejan Aquatic-life-associated 24812 Neisseria gonorrhoeae FA 1090 NC_002946 1 0 patient with disseminated gonococcal infections isolated from a patient with disseminated gonococcal infections Clinical/Human-associated 87511 Neisseria gonorrhoeae NCCP11945 NC_011035,NC_011034 1 1 vaginal smear of a Korean patient isolated in 2002 from a vaginal smear of a Korean patient Clinical/Human-associated 174987 Neisseria gonorrhoeae TCDC-NG08107 NC_017511 1 0 male patient isolated from a male patient in May 2008 Clinical/Human-associated 170077 Neisseria lactamica 020-06 NC_014752 1 0 nasopharyngeal culture isolated from a nasopharyngeal culture Clinical/Human-associated 117761 Neisseria meningitidis 053442 NC_010120 1 0 2003-2005 outbreak of meningococcal disease in China Clinical/Human-associated 144578 Neisseria meningitidis 8013 NC_017501 1 0 blood of a 57-year-old male at the Institut Pasteur Clinical/Human-associated 141067 Neisseria meningitidis alpha14 NC_013016 1 0 isolated from healthy carriers during a carriage study performed in 1999/2000 in Bavaria, Germany Clinical/Human-associated 23504 Neisseria meningitidis alpha710 NC_017505 1 0 Clinical/Human-associated 17609 Neisseria meningitidis FAM18 NC_008767 1 0 patient with meningococcal septicemia isolated from a patient with meningococcal septicemia Clinical/Human-associated 175532 Neisseria meningitidis G2136 NC_017513 1 0 Isolated in United Kingdom in 1986. Human nasopharynx Clinical/Human-associated 174185 Neisseria meningitidis H44/76 NC_017516 1 0 Isolated in Norway in 1976. Human nasopharynx Clinical/Human-associated 175098 Neisseria meningitidis M01-240149 NC_017514 1 0 Isolated in United Kindom in 2001. Human nasopharynx Clinical/Human-associated 181352 Neisseria meningitidis M01-240355 NC_017517 1 0 Isolated in United Kingdom in 2001. Human nasopharynx Clinical/Human-associated 179694 Neisseria meningitidis M04-240196 NC_017515 1 0 Isolated in United Kingdom in 2004. Human nasopharynx Clinical/Human-associated 85645 Neisseria meningitidis MC58 NC_003112 1 0 case of invasive infection isolated from a case of invasive infection Clinical/Human-associated 179262 Neisseria meningitidis NZ-05/33 NC_017518 1 0 Isolated in New Zealand in 2005. Human nasopharynx Clinical/Human-associated 180999 Neisseria meningitidis WUE 2594 NC_017512 1 0 Isolated in Germany in 1991 from a patient suffering from acute bacterial meningitis. Human nasopharynx Clinical/Human-associated 132687 Neisseria meningitidis Z2491 NC_003116 1 0 isolated in Gambia in 1983 Clinical/Human-associated 104330 Neorickettsia risticii str. Illinois NC_013009 1 0 horse blood isolated from horse blood in Maryland Terrestrial-animal-associated 119815 Neorickettsia sennetsu str. Miyayama NC_007798 1 0 Clinical/Human-associated 154066 Niastella koreensis GR20-10 NC_016609 1 0 Soil cultivated with Korean ginseng; Yeongju region of Korea Plant/agriculture-associated 150288 Nitratifractor salsuginis DSM 16511 NC_014935 1 0 Deep-sea hydrothermal vent chimney at the summits of the sulfide mounds in the sediment-hosted back-arc hydrothermal system Iheya North Extreme-environment 82229 Nitratiruptor sp. SB155-2 NC_009662 1 0 deep-sea hydrothermal vent isolated from a deep-sea hydrothermal vent in the Iheya North field in the Mid-Okinawa Trough as part of a larger diversity study Extreme-environment 61822 Nitrobacter hamburgensis X14 NC_007964,NC_007959,NC_007960,NC_007961 1 3 soil isolated from soil and will be used for comparative genomics with other Nitrobacter spp soil 102302 Nitrobacter winogradskyi Nb-255 NC_007406 1 0 Obtained from the American Type Culture Collection as strain ATCC 25391 unknown 115488 Nitrosococcus halophilus Nc4 NC_013958,NC_013960 1 1 a salt lagoon off Sardinia in the Mediterranean Sea, respectively Aquatic-environment 57959 Nitrosococcus oceani ATCC 19707 NC_007484,NC_007483 1 1 marine Aquatic-environment 28885 Nitrosococcus watsonii C-113 NC_014315,NC_014317,NC_014316 1 2 Mediterranean Sea, Port Said Aquatic-environment 56163 Nitrosomonas europaea ATCC 19718 NC_004757 1 0 unknown 7577 Nitrosomonas eutropha C91 NC_008344,NC_008342,NC_008341 1 2 sewage disposal plant isolated from a sewage disposal plant in Chicago Polluted/impacted environment 88817 Nitrosomonas sp. AL212 NC_015221,NC_015222,NC_015223 1 2 laboratory waste water treatment reactor Polluted/impacted environment 114918 Nitrosomonas sp. Is79A3 NC_015731 1 0 freshwater sediment Aquatic-environment 110821 Nitrosospira multiformis ATCC 25196 NC_007614,NC_007615,NC_007616,NC_007617 1 3 soil isolated from soil in Suriname and will be used for comparative genomics with other ammonia-oxidizing bacteria soil Nocardia brasiliensis ATCC 700358 NC_018681 1 0 isolated from a human case Clinical/Human-associated 220957 Nocardia cyriacigeorgica NC_016887.1 1 0 Clinical/Human-associated 94200 Nocardia farcinica IFM 10152 NC_006361,NC_006362,NC_006363 1 2 the bronchus of a male Japanese patient isolated from the bronchus of a male Japanese patient Clinical/Human-associated 122728 Nocardioides sp. JS614 NC_008699,NC_008697 1 1 soil, Carson, CA, USA soil 243618 Nocardiopsis alba ATCC BAA-2165 NC_018524.1 1 0 honeybee guts isolated from honeybee guts Insect-associated/other symbiont 52663 Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111 NC_014210,NC_014211 1 1 Lab/Engineered 87061 Nonlabens dokdonensis DSW-6 NC_020156.1 1 0 Isolated from the surface seawater collected between the two main islands of Dokdo, Republic of Korea. Aquatic-environment 102301 'Nostoc azollae' 0708 NC_014248,NC_014249,NC_014250 1 2 water fern Azolla filiculoides commonly known as duckweed Plant/agriculture-associated 48114 Nostoc punctiforme PCC 73102 NC_010628,NC_010632,NC_010630,NC_010633,NC_010629,NC_010631 1 5 symbiotic association with the gymnosperm cycad Macrozamia sp isolated from a symbiotic association with the gymnosperm cycad Macrozamia sp Plant/agriculture-associated 89938 Nostoc sp. PCC 7107 NC_019676.1 1 0 water from shallow pond Aquatic-environment 37423 Nostoc sp. PCC 7120 NC_003272,NC_003276,NC_003240,NC_003267,NC_003273,NC_003270,NC_003241 1 6 fresh water Aquatic-environment 50627 Novosphingobium aromaticivorans DSM 12444 NC_007794,NC_009427,NC_009426 1 2 sample obtained at a depth of 410 m from a borehole sample that was drilled at the Savannah River Site isolated from a sample obtained at a depth of 410 m from a borehole sample that was drilled at the Savannah River Site in South Carolina, USA, by the Department of Energy Aquatic-environment 152401 Novosphingobium sp. PP1Y NC_015580,NC_015579,NC_015582,NC_015583 1 3 isolated from seawater from the harbor of Pozzuoli (Naples, Italy) Aquatic-environment 1263 Oceanimonas sp. GK1 NC_016745,NC_016746,NC_016747 1 2 isolated from Gavkhouni Wetland in Iran Extreme-environment 145519 Oceanithermus profundus DSM 14977 NC_014753,NC_014761 1 1 Deep-sea hot vent; 13N, East Pacific Rise Extreme-environment 82024 Oceanobacillus iheyensis HTE831 NC_004193 1 0 deep sea mud (1050 m) from the Iheya ridge near Okinawa, Japan isolated from deep sea mud (1050 m) from the Iheya ridge near Okinawa, Japan in 1998 Aquatic-environment 73124 Ochrobactrum anthropi ATCC 49188 NC_009667,NC_009668,NC_009671,NC_009672,NC_009669,NC_009670 2 4 Arsenical cattle-dipping fluid Polluted/impacted environment 147623 Odoribacter splanchnicus DSM 20712 NC_015160 1 0 wound Clinical/Human-associated 113004 Oenococcus oeni PSU-1 NC_008528 1 0 isolated at Penn State University and is used commercially for malolactic fermentation in wines unknown 196796 Oligotropha carboxidovorans OM4 NC_017538,NC_017536,NC_017539 1 2 Isolated in 1978 from wastewater in Goettingen, Germany. Polluted/impacted environment 134280 Oligotropha carboxidovorans OM5 NC_011386 1 0 Extreme-environment 203740 Oligotropha carboxidovorans OM5 NC_015684.1,NC_015689.1,NC_015685.1 1 2 Isolated in 1978 from wastewater in Goettingen, Germany. Polluted/impacted environment 28891 Olsenella uli DSM 7084 NC_014363 1 0 plaque from human gingival crevices Clinical/Human-associated 86799 Onion yellows phytoplasma OY-M NC_005303 1 0 wild-type disease-causing strain (OY-W; onions yellow disease) derived from a wild-type disease-causing strain (OY-W; onions yellow disease) which was isolated in Saga Prefecture, Japan, in 1982, and shows mild symptoms and does not cause stunting nor phloem hyperplasia (excessive increase in number of cells) Plant/agriculture-associated 17422 Opitutus terrae PB90-1 NC_010571 1 0 rice paddy soil Plant/agriculture-associated 83812 Orientia tsutsugamushi str. Boryong NC_009488 1 0 human isolated from a human in 1995 in Boryong, Korea Clinical/Human-associated 129072 Orientia tsutsugamushi str. Ikeda NC_010793 1 0 Clinical/Human-associated 164984 Ornithobacterium rhinotracheale DSM 15997 NC_018016.1 1 0 Terrestrial-animal-associated 116170 Oscillatoria acuminata PCC 6304 NC_019693.1,NC_019700.1,NC_019694.1 1 2 soil soil 7962 Oscillatoria nigro-viridis PCC 7112 NC_019729.1,NC_019731.1,NC_019764.1,NC_019763.1,NC_019732.1,NC_019730.1 1 5 soil in orchid house soil 200622 Owenweeksia hongkongensis DSM 17368 NC_016599 1 0 Sea water (sand filtered); China, Hong Kong Aquatic-environment 151357 Paenibacillus larvae subsp. larvae DSM 25430 NC_023134.1,NC_023147.1 1 1 AFB-diseased colony Insect-associated/other symbiont 230942 Paenibacillus mucilaginosus 3016 NC_016935.1 1 0 rhizosphere soil and widely used isolated from rhizosphere soil and widely used in microbial fertilizer for most manufacturers in China Plant/agriculture-associated 184456 Paenibacillus mucilaginosus K02 NC_017672.1 1 0 Plant/agriculture-associated 192881 Paenibacillus mucilaginosus KNP414 NC_015690 1 0 Growth-Improving unknown 319074 Paenibacillus polymyxa CR1 NC_023037.1 1 0 Plant/agriculture-associated 94484 Paenibacillus polymyxa E681 NC_014483 1 0 Plant/agriculture-associated 118909 Paenibacillus polymyxa M1 NC_017542,NC_017543 1 1 Isolated from surface-sterilized wheat root tissues. Plant/agriculture-associated 172748 Paenibacillus polymyxa SC2 NC_014622,NC_014628 1 1 Plant/agriculture-associated 118865 Paenibacillus sp. JDR-2 NC_012914 1 0 sweet gum stem wood buried isolated from sweet gum stem wood buried in surface soil Plant/agriculture-associated 56627 Paenibacillus sp. Y412MC10 NC_013406 1 0 Plant/agriculture-associated 182166 Paenibacillus terrae HPL-003 NC_016641 1 0 Plant/agriculture-associated 155528 Paludibacter propionicigenes WB4 NC_014734 1 0 plant residues in an anoxic rice-field soil Plant/agriculture-associated 322955 Pandoraea pnomenusa 3kgm NC_022904.1 1 0 soil solated from a Former Landfill Site Polluted/impacted environment 318770 Pandoraea sp. RB-44 NC_023018.1 1 0 landfill duming ground soil Polluted/impacted environment 225404 Pantoea ananatis NC_016816.1,NC_016817.1 1 0 isolated from a human wound Clinical/Human-associated 188453 Pantoea ananatis AJ13355 NC_017531,NC_017533 1 1 biotechnological potential isolated from soil soil 151616 Pantoea ananatis LMG 20103 NC_013956 1 0 isolated from diseased Eucalyptus in South Africa isolated from an outbreak of Eucalyptus blight and dieback in South Africa, causing major economic losses of this important forestry crop Plant/agriculture-associated 213218 Pantoea ananatis PA13 NC_017554,NC_017553 1 1 Isolated from a diseased rice grain. Plant/agriculture-associated 129740 Pantoea sp. At-9b NC_014837,NC_014842,NC_014841,NC_014840,NC_014839,NC_014838 1 5 Plant/agriculture-associated Pantoea vagans C9-1 NC_014562,NC_014561,NC_014563,NC_014258 1 3 Isolated from Michigan-grown apple (Malus x domestica 'Jonathan') stem tissue. Plant/agriculture-associated 29947 Parabacteroides distasonis ATCC 8503 NC_009615 1 0 Clinical/Human-associated 162898 Parachlamydia acanthamoebae UV7 NC_015702 1 0 Clinical/Human-associated 315434 Paracoccus aminophilus JCM 7686 NC_022041.1,NC_022044.1,NC_022050.1,NC_022043.1,NC_022042.1,NC_022049.1 1 5 soil soil 97112 Paracoccus denitrificans PD1222 NC_008686,NC_008688,NC_008687 2 1 genetically modified version of strain DSM 413 (type strain) Lab/Engineered 90819 Parvibaculum lavamentivorans DS-1 NC_009719 1 0 Activated sludge Polluted/impacted environment 119301 Parvularcula bermudensis HTCC2503 NC_014414 1 0 isolated from the Sargasso Sea Aquatic-environment 218540 Pasteurella multocida 36950 NC_016808 1 0 Originated from a case of bovine respiratory tract infection. Terrestrial-animal-associated 133987 Pasteurella multocida subsp. multocida str. 3480 NC_017764.1 1 0 the lung of a pig with pneumonia isolated from the lung of a pig with pneumonia Terrestrial-animal-associated 234296 Pasteurella multocida subsp. multocida str. HN06 NC_017027.1,NC_017035.1 1 1 diseased pig isolated in 2003 from a diseased pig Terrestrial-animal-associated 88067 Pasteurella multocida subsp. multocida str. Pm70 NC_002663 1 0 case of fowl cholera isolated in 1995 from a case of fowl cholera in chickens Terrestrial-animal-associated 54885 Pectobacterium atrosepticum SCRI1043 NC_004547 1 0 the stem of a potato plant isolated from the stem of a potato plant Plant/agriculture-associated 70489 Pectobacterium carotovorum subsp. carotovorum PC1 NC_012917 1 0 Plant/agriculture-associated 258068 Pectobacterium carotovorum subsp. carotovorum PCC21 NC_018525.1 1 0 Isolated from a plant in Korea Plant/agriculture-associated 236945 Pectobacterium sp. SCC3193 NC_017845.1 1 0 potato isolated from potato in Finland Plant/agriculture-associated 23660 Pectobacterium wasabiae WPP163 NC_013421 1 0 Plant/agriculture-associated 151045 Pediococcus claussenii ATCC BAA-344 NC_016605,NC_016635,NC_016606,NC_016607,NC_016608,NC_016636,NC_017017,NC_017018,NC_017019 1 8 brewery isolate which has a ropy phenotype Production-site-facility 34213 Pediococcus pentosaceus ATCC 25745 NC_008525 1 0 unknown 311725 Pediococcus pentosaceus SL4 NC_022780.1 1 0 isolated from a Korean fermented vegetable product, kimchi Food-associated 98714 Pedobacter heparinus DSM 2366 NC_013061 1 0 dry soil soil 163994 Pedobacter saltans DSM 12145 NC_015177 1 0 soil soil 211702 Pelagibacterium halotolerans B2 NC_016078,NC_016079 1 1 East China Sea Isolated from a seawater sample from a depth of 70 m in the East China Sea. Aquatic-environment 86875 Pelobacter carbinolicus DSM 2380 NC_007498 1 0 mud isolated from mud in Venice, Italy Aquatic-environment 64470 Pelobacter propionicus DSM 2379 NC_008609,NC_008607,NC_008608 1 2 crrek mud Aquatic-environment 134556 Pelodictyon phaeoclathratiforme BU-1 NC_011060 1 0 lake water isolated from lake water in 1989 Aquatic-environment 8413 Pelotomaculum thermopropionicum SI NC_009454 1 0 granular sludge from a thermophilic upflow anaerobic sludge blanket (UASB) reactor isolated from granular sludge from a thermophilic upflow anaerobic sludge blanket (UASB) reactor Polluted/impacted environment 119911 Persephonella marina EX-H1 NC_012440,NC_012439 1 1 deep sea hydrothermal vent collected from a deep sea hydrothermal vent on the East Pacific Rise. and isolated by dilution to extinction methods. Extreme-environment 40494 Petrotoga mobilis SJ95 NC_010003 1 0 the production waters of a North Sea oil reservoir isolated from the production waters of a North Sea oil reservoir Extreme-environment 319425 Phaeobacter gallaeciensis DSM 26640 NC_023137.1,NC_023141.1,NC_023143.1,NC_023139.1,NC_023138.1,NC_023148.1,NC_023140.1,NC_023142.1 1 7 scallop Terrestrial-animal-associated 44517 Phenylobacterium zucineum HLK1 NC_011144,NC_011143 1 1 isolated from human erythroleukemia cell line K562 Clinical/Human-associated 109272 Photobacterium profundum SS9 NC_006370,NC_006371,NC_005871 2 1 the Sulu Trough isolated at a depth of 2500 m from the Sulu Trough Aquatic-environment 71438 Photorhabdus asymbiotica NC_012962,NC_012961 1 1 human blood isolate from human blood Clinical/Human-associated 48522 Photorhabdus luminescens subsp. laumondii TTO1 NC_005126 1 0 Isolated from the nematode Heterorhabditis bacteriophora on Trinidad and Tobago Insect-associated/other symbiont 4342 Pirellula staleyi DSM 6068 NC_013720 1 0 Freshwater Lake Lansing, Michigan Aquatic-environment 152897 Planctomyces brasiliensis DSM 5305 NC_015174 1 0 Water from salt pit, Lagoa Vermelha, Brazil Extreme-environment 6916 Planctomyces limnophilus DSM 3776 NC_014148,NC_014149 1 1 surface water isolated from surface water and will be used for comparative analysis Aquatic-environment Plautia stali symbiont NC_022546,NC_022533,NC_022534 1 2 endosymbiont Insect-associated/other symbiont 50427 Pleurocapsa sp. PCC 7327 NC_019689.1 1 0 spring water (Hunter's hot spring) Extreme-environment 76733 Polaromonas naphthalenivorans CJ2 NC_008781,NC_008758,NC_008759,NC_008760,NC_008761,NC_008762,NC_008763,NC_008764,NC_008757 1 8 Naphthalene-contaminated freshwater sediment Polluted/impacted environment 102244 Polaromonas sp. JS666 NC_007948,NC_007949,NC_007950 1 2 sediment contaminated with cis-dichloroethane (cDCE), a common pollutant resulting from widespread manufacture and use of industrial solvents isolated from sediment contaminated with cis-dichloroethane (cDCE), a common pollutant resulting from widespread manufacture and use of industrial solvents Polluted/impacted environment 182274 Polymorphum gilvum SL003B-26A1 NC_015258,NC_015259 1 1 crude oil-polluted saline soil isolated from a crude oil-polluted saline soil in Shengli Oilfield, China and could use the crude oil as the sole carbon source Polluted/impacted environment 12025 Polynucleobacter necessarius subsp. asymbioticus QLW-P1DMWA-1 NC_009379 1 0 Acidic freshwater pond; Austrian Alps, 1300 meters above sea level Extreme-environment 8289 Polynucleobacter necessarius subsp. necessarius STIR1 NC_010531 1 0 cilliate Euplotes aediculatus Aquatic-life-associated 172508 Porphyromonas asaccharolytica DSM 20707 NC_015501 1 0 Empyema Clinical/Human-associated 26334 Porphyromonas gingivalis ATCC 33277 NC_010729 1 0 human gingiva is being sequenced for comparative genome analysis isolated from human gingiva is being sequenced for comparative genome analysis Clinical/Human-associated 195531 Porphyromonas gingivalis TDC60 NC_015571 1 0 severe human periodontal lesion at Tokyo Dental College in Japan Clinical/Human-associated 134034 Porphyromonas gingivalis W83 NC_002950 1 0 unknown human infection isolated by H. Werner in the 1950s in Bonn, Germany, from an unknown human infection Clinical/Human-associated 163057 Prevotella denticola F0289 NC_015311 1 0 Dewhirst Lab Human oral cavity Clinical/Human-associated 47739 Prevotella melaninogenica ATCC 25845 NC_014370,NC_014371 2 0 Human oral flora Clinical/Human-associated 14515 Prevotella ruminicola 23 NC_014033 1 0 gastrointestinal isolate Clinical/Human-associated 75723 Prochlorococcus marinus str. AS9601 NC_008816 1 0 Arabian Sea at a depth of 50 meter collected in the Arabian Sea at a depth of 50 meters and isolated by filter fractionation Aquatic-environment 136502 Prochlorococcus marinus str. MIT 9211 NC_009976 1 0 the equatorial Pacific at a depth of 83 meters isolated from the equatorial Pacific at a depth of 83 meters by filter fractionation Aquatic-environment 119824 Prochlorococcus marinus str. MIT 9215 NC_009840 1 0 5m depth at Equatorial Pacific on October 1992 Aquatic-environment 103344 Prochlorococcus marinus str. MIT 9301 NC_009091 1 0 the Sargasso Sea at a depth of 90 m (34o 45 isolated from the Sargasso Sea at a depth of 90 m (34o 45 Aquatic-environment 17757 Prochlorococcus marinus str. MIT 9303 NC_008820 1 0 Sargasso Sea at a depth of 100 m collected from the Sargasso Sea at a depth of 100 m and was isolated by filter fractionation. Aquatic-environment 70153 Prochlorococcus marinus str. MIT 9312 NC_007577 1 0 Gulf Stream in the north Atlantic Ocean collected from the Gulf Stream in the north Atlantic Ocean. Aquatic-environment 135351 Prochlorococcus marinus str. MIT 9313 NC_005071 1 0 Isolated from a depth of 135m in the Gulf Stream in 1992. Aquatic-environment 113831 Prochlorococcus marinus str. MIT 9515 NC_008817 1 0 surface waters of the Equatorial Pacific collected from the surface waters of the Equatorial Pacific, and isolated by filter fractionation Aquatic-environment 31285 Prochlorococcus marinus str. NATL1A NC_008819 1 0 depth of 30 meters in the north Atlantic Ocean collected at a depth of 30 meters in the north Atlantic Ocean Aquatic-environment 14922 Prochlorococcus marinus str. NATL2A NC_007335 1 0 depth of 30 meters in the north Atlantic Ocean collected at a depth of 30 meters in the north Atlantic Ocean Aquatic-environment 8617 Prochlorococcus marinus subsp. marinus str. CCMP1375 NC_005042 1 0 deep euphotic zone in sea Aquatic-environment 68066 Prochlorococcus marinus subsp. pastoris str. CCMP1986 NC_005072 1 0 5m depth in Mediterranean Sea Aquatic-environment 237183 Propionibacterium acidipropionici ATCC 4875 NC_019395.1 1 0 Emmental cheese Food-associated 172619 Propionibacterium acnes 266 NC_017534 1 0 pleuropulmonary infection isolate from a pleuropulmonary infection Clinical/Human-associated 190978 Propionibacterium acnes 6609 NC_017535 1 0 Recovered from a skin sample from a woman with no recorded acne history. patient with inflammatory acne Clinical/Human-associated 207611 Propionibacterium acnes ATCC 11828 NC_017550 1 0 Recovered from a subcutaneous abscess. Clinical/Human-associated 260395 Propionibacterium acnes C1 NC_018707.1 1 0 sarcoidosis patient isolate from sarcoidosis patient Clinical/Human-associated 237405 Propionibacterium acnes HL096PA1 NC_021085.1,NC_021086.1 1 1 Clinical/Human-associated 64440 Propionibacterium acnes KPA171202 NC_006085 1 0 human skin Isolated from human skin, this strain is used for comparative genomics Clinical/Human-associated 10541 Propionibacterium acnes SK137 NC_014039 1 0 Acne vulgaris, folliculitis, sarcoidosis, system infection and endocarditis, postoperative infections Clinical/Human-associated 219018 Propionibacterium acnes TypeIA2 P.acn17 NC_016512 1 0 recovered from ophthalmic infections Clinical/Human-associated 223513 Propionibacterium acnes TypeIA2 P.acn31 NC_016511 1 0 recovered from ophthalmic infections Clinical/Human-associated 219306 Propionibacterium acnes TypeIA2 P.acn33 NC_016516 1 0 recovered from ophthalmic infections Clinical/Human-associated 230658 Propionibacterium avidum 44067 NC_021064.1 1 0 Clinical/Human-associated 163322 Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1 NC_014215 1 0 a Hardy Actinobacterium with Food and Probiotic Applications unknown 161471 Propionibacterium propionicum F0230a NC_018142 1 0 Human oral cavity Clinical/Human-associated 37017 Prosthecochloris aestuarii DSM 271 NC_011059,NC_011061 1 1 isolated from the hydrogen sulfide-rich mud of a shallow lagoon with elevated salt concentration and described in 1970 by Gorlenko Polluted/impacted environment 286397 Proteus mirabilis BB2000 NC_022000.1 1 0 isolated as described in Belas et al Clinical/Human-associated 120933 Proteus mirabilis HI4320 NC_010554,NC_010555 1 1 human urinary tract Proteus mirabilis is a tetracycline resistant human urinary tract isolate. Clinical/Human-associated 236675 Providencia stuartii MRSN 2154 NC_017731.1 1 0 blood isolated from an Afghan national Clinical/Human-associated 137209 Pseudanabaena sp. PCC 7367 NC_019701.1,NC_019690.1 1 1 a snail shell, intertidal zone in Mexico Aquatic-life-associated 25434 Pseudoalteromonas atlantica T6c NC_008228 1 0 biofilm from San Diego Bay isolated from a biofilm from San Diego Bay in California Aquatic-environment 105694 Pseudoalteromonas haloplanktis TAC125 NC_007481,NC_007482 2 0 sample of coastal sea water near a French Antarctic station (66O40' S; 140O 01' E near Dumont d'Urville) isolated from a sample of coastal sea water near a French Antarctic station (66O40' S; 140O 01' E near Dumont d'Urville) Aquatic-environment 136886 Pseudoalteromonas sp. SM9913 NC_014800,NC_014803 2 0 isolated from deep-sea sediment at a water depth of 1855 meters near the Okinawa Trough Aquatic-environment 173302 Pseudogulbenkiania sp. NH8B NC_016002 1 0 Originally isolated from an agricultural field in Niigata, Japan, where paddy rice and soybean were rotationally cultivated every 2 years. isolated from an agricultural field Plant/agriculture-associated 282598 Pseudomonas aeruginosa B136-33 NC_020912.1 1 0 infant with community-acquired diarrhea isolate from an infant with community-acquired diarrhea Clinical/Human-associated 309598 Pseudomonas aeruginosa c7447m NC_022360 1 0 patient with a chronic lung infection with P isolate from a patient with a chronic lung infection with P. aeruginosa Clinical/Human-associated 240047 Pseudomonas aeruginosa DK2 NC_018080.1 1 0 cystic fibrosis patient isolated from a cystic fibrosis patient Clinical/Human-associated 318984 Pseudomonas aeruginosa LES431 NC_023066.1 1 0 Clinical/Human-associated 113719 Pseudomonas aeruginosa LESB58 NC_011770 1 0 isolated at the Liverpool Cystic Fibrosis (CF) clinic center Clinical/Human-associated 178473 Pseudomonas aeruginosa M18 NC_017548 1 0 isolated from sweet melon rhizosphere in Shanghai suburb in 1996 Plant/agriculture-associated Pseudomonas aeruginosa MTB-1 NC_023019 1 0 Isolated from a Microbial Community Enriched by the Technical Formulation of Hexachlorocyclohexane denitrification Polluted/impacted environment 209107 Pseudomonas aeruginosa NCGM2.S1 NC_017549 1 0 Homo sapiens a representative strain of a cluster endemic to Japan. Clinical/Human-associated 319395 Pseudomonas aeruginosa PA1 NC_022808.1 1 0 isolated at the second affiliated hospital of the Third Military Medical University, Chongqing, China Clinical/Human-associated 322742 Pseudomonas aeruginosa PA1R NC_022806.1 1 0 red mutant strain Lab/Engineered 80442 Pseudomonas aeruginosa PA7 NC_009656 1 0 Clinical/Human-associated isolate This strain is a Clinical/Human-associated isolate Clinical/Human-associated 58763 Pseudomonas aeruginosa PAO1 NC_002516 1 0 human infected wound Clinical/Human-associated 305084 Pseudomonas aeruginosa PAO1-VE13 NC_022594 1 0 Mutant strain Lab/Engineered 310614 Pseudomonas aeruginosa PAO1-VE2 NC_022591.1 1 0 Mutant strain Lab/Engineered 314125 Pseudomonas aeruginosa PAO581 NC_022361.1 1 0 derived from the parental strain PAO1 Lab/Engineered 293239 Pseudomonas aeruginosa RP73 NC_021577.1 1 0 patient with Cystic Fibrosis isolate from a patient with Cystic Fibrosis Clinical/Human-associated 322054 Pseudomonas aeruginosa SCV20265 NC_023149.1 1 0 isolated from a cystic fibrosis (CF) patient Clinical/Human-associated 79785 Pseudomonas aeruginosa UCBPP-PA14 NC_008463 1 0 human burn patient isolate from a human burn patient Clinical/Human-associated 188168 Pseudomonas brassicacearum subsp. brassicacearum NFM421 NC_015379 1 0 laboratory strain Lab/Engineered 200981 Pseudomonas chlororaphis O6 NZ_CM001490.1 1 0 the soil isolated from the soil in Utah, USA (DOI: 10 soil 287894 Pseudomonas denitrificans ATCC 13867 NC_020829.1 1 0 industrial strain unknown 83862 Pseudomonas entomophila L48 NC_008027 1 0 environmental isolate, soil soil 200956 Pseudomonas fluorescens A506 NC_017911.1 1 0 leaf of a pear tree isolated from a leaf of a pear tree in California, USA (PMID:16349371), and is a commercial biological control agent used primarily for the suppression of fire blight on pear and apple, which is caused by the plant pathogenic bacterium Erwinia amylovora (PMID:18944382) Plant/agriculture-associated 223857 Pseudomonas fluorescens F113 NC_016830 1 0 sugar-beet rhizosphere Plant/agriculture-associated 44242 Pseudomonas fluorescens Pf0-1 NC_007492 1 0 agricultural loam (sand, clay, and organic matter) soil isolated from agricultural loam (sand, clay, and organic matter) soil in 1988 by Compeau et al Plant/agriculture-associated 72549 Pseudomonas fluorescens Pf-5 NC_004129 1 0 root surface of cotton Plant/agriculture-associated 98510 Pseudomonas fluorescens SBW25 NC_012660,NC_009444 1 1 field-grown sugar beet isolated from a field-grown sugar beet Plant/agriculture-associated 161978 Pseudomonas fulva 12-X NC_015556 1 0 rice plants Plant/agriculture-associated 187712 Pseudomonas mendocina NK-01 NC_015410 1 0 farmland soil in Tianjin, China Plant/agriculture-associated 131592 Pseudomonas mendocina ymp NC_009439 1 0 sediment, surface holding pond, Nevada Test Site, NV Aquatic-environment 322611 Pseudomonas monteilii SB3078 NC_023075.1 1 0 isolated from motor oil-contaminated soil (Salem, VA, USA, June 1992) Polluted/impacted environment 325022 Pseudomonas monteilii SB3101 NC_023076.1 1 0 isolated from motor oil-contaminated soil (Salem, VA, USA, June 1992) Polluted/impacted environment 269174 Pseudomonas poae RE*1-1-14 NC_020209.1 1 0 endorhiza sugar beet Plant/agriculture-associated 238813 Pseudomonas protegens CHA0 NC_021237.1 1 0 the roots of tobacco isolated in 1983 from the roots of tobacco in a soil suppressive to Thielaviopsis basicola (black root rot of tobacco) in Morens, Switzerland Plant/agriculture-associated 176522 Pseudomonas putida BIRD-1 NC_017530 1 0 rhizosphere of a plant Plant/agriculture-associated 243421 Pseudomonas putida DOT-T1E NC_018220.1 1 0 "P. putida strain that wasisolated from a wastewater treatment plant" Polluted/impacted environment 56420 Pseudomonas putida F1 NC_009512 1 0 polluted creek isolated from a polluted creek in Urbana, Illinois by enrichment culture with ethylbenzyne as a sole source of carbon and energy Polluted/impacted environment 76638 Pseudomonas putida GB-1 NC_010322 1 0 fresh water Aquatic-environment 293256 Pseudomonas putida H8234 NC_021491.1 1 0 Hospital of Besancon Clinical/Human-associated 258503 Pseudomonas putida HB3267 NC_019905.1 1 0 Isolated from a patient in a hospital Clinical/Human-associated 30601 Pseudomonas putida KT2440 NC_002947 1 0 toluene-degrading isolate, Pseudomonas arvilla strain mt-2 (renamed Pseudomonas putida mt-2), derived from a toluene-degrading isolate, Pseudomonas arvilla strain mt-2 (renamed Pseudomonas putida mt-2), by loss of its plasmid Polluted/impacted environment 256897 Pseudomonas putida NBRC 14164 NC_021505.1 1 0 unknown 3905 Pseudomonas putida ND6 NC_017986.1,NC_005244,NC_018746 1 2 industrial wastewater Polluted/impacted environment 201901 Pseudomonas putida S16 NC_015733 1 0 A soil sample (0.5 g, wet weight) from a field under continuous tobacco cropping in Shandong, People's Republic of China soil 93764 Pseudomonas putida W619 NC_010501 1 0 Black Cottonwood tree isolated from the Black Cottonwood tree and is closely related to other endophytic and rhizosphere strains of Pseudomonas putida Plant/agriculture-associated 261259 Pseudomonas resinovorans NBRC 106553 NC_021499.1,NC_021506.1 1 1 isolated from activated sludge Polluted/impacted environment 321350 Pseudomonas sp. TKP NC_023064.1 1 0 isolated from a γ-Hexachlorocyclohexane-Degrading Mixed Culture Polluted/impacted environment 243240 Pseudomonas sp. UW4 NC_019670.1 1 0 isolated from the rhizosphere of reeds in Waterloo, Ontario Plant/agriculture-associated 43816 Pseudomonas sp. VLB120 NC_022738.1,NC_022739.1 1 1 soil isolated from soil soil 31643 Pseudomonas stutzeri A1501 NC_009434 1 0 rice roots that had been inoculated with strain A15 isolated from rice roots that had been inoculated with strain A15 in a rice paddy in China Plant/agriculture-associated 9221 Pseudomonas stutzeri ATCC 17588 = LMG 11199 NC_015740 1 0 Human spinal fluid Clinical/Human-associated 243261 Pseudomonas stutzeri CCUG 29243 NC_018028.1 1 0 sediments of the West Mediterranean Sea isolated from sediments of the West Mediterranean Sea Aquatic-environment 231459 Pseudomonas stutzeri DSM 10701 NC_018177.1 1 0 anaerobic enrichment of soil with succinate and nitrous oxide isolated from an anaerobic enrichment of soil with succinate and nitrous oxide Polluted/impacted environment 183391 Pseudomonas stutzeri DSM 4166 NC_017532 1 0 Isolated from the rhizosphere of a high-fixing Sorghum nutans cultivar in Germany. Plant/agriculture-associated 180717 Pseudomonas stutzeri RCH2 NC_019936.1,NC_019938.1,NC_019937.1,NC_019939.1 1 3 Cr-contaminated aquifer. Polluted/impacted environment 11986 Pseudomonas synxantha BG33R NZ_CM001514.1 1 0 the rhizosphere of a peach tree isolated from the rhizosphere of a peach tree in an orchard near Elgin, South Carolina, USA (Kluepfel et al Plant/agriculture-associated 78478 Pseudomonas syringae pv. phaseolicola 1448A NC_005773,NC_007274,NC_007275 1 2 Plant/agriculture-associated 42314 Pseudomonas syringae pv. syringae B728a NC_007005 1 0 snap bean leaflet isolated from a snap bean leaflet in Wisconsin Plant/agriculture-associated 93040 Pseudomonas syringae pv. tomato str. DC3000 NC_004578,NC_004633,NC_004632 1 2 Plant/agriculture-associated 141225 Pseudonocardia dioxanivorans CB1190 NC_015312,NC_015314,NC_015313 1 2 Industrial sludge contaminated with 1,4-dioxane Polluted/impacted environment 224584 Pseudovibrio sp. FO-BEG1 NC_016642,NC_016646 1 1 Isolated with Beggiatoa sp. from a black band diseased coral Aquatic-life-associated 216031 Pseudoxanthomonas spadix BD-a59 NC_016147 1 0 isolated from gasoline-contaminated sediment Polluted/impacted environment 172708 Pseudoxanthomonas suwonensis 11-1 NC_014924 1 0 bioreactor Polluted/impacted environment 98534 Psychrobacter arcticus 273-4 NC_007204 1 0 20-40000 year old Serbian permafrost in Russia, Siberia, Kolyma lowland Extreme-environment 128170 Psychrobacter cryohalolentis K5 NC_007969,NC_007968 1 1 saline liquid (12-14%) found 11-24 m below the surface within a forty thousand-year-old Siberian permafrost at the Kolyma-Indigirka lowland isolated from saline liquid (12-14%) found 11-24 m below the surface within a forty thousand-year-old Siberian permafrost at the Kolyma-Indigirka lowland in Siberia Extreme-environment 4273 Psychrobacter sp. G NC_021661.1,NC_021662.1,NC_021669.1,NC_021668.1 1 3 isolated from King George Island, Antarctica Extreme-environment 74803 Psychrobacter sp. PRwf-1 NC_009524,NC_009516,NC_009517 1 2 Skin and gills of Lutjanus vivanus Skin and gills of Lutjanus vivanus, off the coast of Lo??za, northeastern Puerto Rico. Aquatic-life-associated 103130 Psychromonas ingrahamii 37 NC_008709 1 0 sea ice, off Point Barrow isolated from sea ice, off Point Barrow in northern Alaska Aquatic-environment 189076 Pusillimonas sp. T7-7 NC_015458,NC_015459 1 1 benthal mud of petroleum-contaminated site in Bohai Sea, China Polluted/impacted environment 175761 Rahnella aquatilis CIP 78.65 = ATCC 33071 NC_016818,NC_016835,NC_016819,NC_017092 1 3 Drinking water, France Aquatic-environment 233148 Rahnella aquatilis HX2 NC_017047.1,NC_017060.1,NC_017773.1,NC_017807.1 1 3 soil of grape vineyard Isolated from soil of grape vineyard in Beijing Plant/agriculture-associated 167412 Rahnella sp. Y9602 NC_015061,NC_015062,NC_015063 1 2 DOE Field Research Center (FRC), Oak Ridge, TN (Area 3) isolate from metal- and radionuclide-contaminated soil Polluted/impacted environment 6770 Ralstonia eutropha H16 NC_008313,NC_008314,NC_005241 2 1 sludge isolated from sludge Polluted/impacted environment 24049 Ralstonia eutropha JMP134 NC_007347,NC_007348,NC_007337,NC_007336 2 2 unknown 57998 Ralstonia pickettii 12D NC_012856,NC_012855,NC_012857,NC_012851,NC_012849 2 3 copper-contaminated sediment from a lake isolated from copper-contaminated sediment from a lake in Michigan Polluted/impacted environment 63053 Ralstonia pickettii 12J NC_010682,NC_010678,NC_010683 2 1 copper-contaminated sediment from a lake isolated from copper-contaminated sediment from a lake in Michigan Polluted/impacted environment 304702 Ralstonia pickettii DTP0602 NC_022514.1,NC_022515.1,NC_022513.1 3 0 isolated from a soil sample in Okayama, Japan soil 166517 Ralstonia solanacearum CFBP2957 NC_014307 1 0 infected tomato plants Plant/agriculture-associated 168141 Ralstonia solanacearum CMR15 NC_017559,NC_017589,NC_017558 1 2 tomato with bacterial wilt Plant/agriculture-associated 285511 Ralstonia solanacearum FQY_4 NC_020799,NC_021745 1 1 bacterial wilt Nursery, which is used for evaluating crops resistance to Ralstonia isolated from a bacterial wilt Nursery, which is used for evaluating crops resistance to Ralstonia in tobacco and potatoes breeding in China Plant/agriculture-associated 70888 Ralstonia solanacearum GMI1000 NC_003295,NC_003296 1 1 tomato plant isolated from the tomato plant and is also pathogenic on Arabidopsis thaliana Plant/agriculture-associated 193606 Ralstonia solanacearum Po82 NC_017574,NC_017575 1 1 potato in Mexico Plant/agriculture-associated 167236 Ralstonia solanacearum PSI07 NC_014311,NC_014310 1 1 tomato with bacterial wilt Plant/agriculture-associated 73150 Ramlibacter tataouinensis TTB310 NC_015677 1 0 subsurface desert soil from Tunisia, Isolated from sand particles coated on a meteorite fragment buried in a sandy soil of a semi-arid region of South Tunisia (Tataouine). soil 276362 Raoultella ornithinolytica B6 NC_021066.1 1 0 Oil-Contaminated Soil Polluted/impacted environment 21953 Renibacterium salmoninarum ATCC 33209 NC_010168 1 0 Yearling chinook salmon at a salmon hatchery in Western Oregon Aquatic-life-associated 298076 Rhizobium etli bv. mimosae str. Mim1 NC_021905.1,NC_021911.1,NC_021908.1,NC_021907.1,NC_021906.1,NC_021910.1,NC_021909.1 1 6 isolated in Huautla, Morelos, Mexico Plant/agriculture-associated 108884 Rhizobium etli CFN 42 NC_007761,NC_007762,NC_007763,NC_007764,NC_004041,NC_007765,NC_007766 1 6 bean Phaseolus vulgaris, Guanajuato Mexico Plant/agriculture-associated 120572 Rhizobium etli CIAT 652 NC_010994,NC_010996,NC_010997,NC_010998 1 3 bean phaseolus vulgaris Plant/agriculture-associated 48398 Rhizobium leguminosarum bv. trifolii WSM1325 NC_012850,NC_012848,NC_012852,NC_012853,NC_012858,NC_012854 1 5 Livadi beach, Serifos, Cyclades, Greece isolated from root nodules collected in 1993 from the Greek Island of Serifos Plant/agriculture-associated 95088 Rhizobium leguminosarum bv. trifolii WSM2304 NC_011369,NC_011366,NC_011371,NC_011370,NC_011368 1 4 isolated from Trifolium polymorphum in Uruguay in 1998 Plant/agriculture-associated 32091 Rhizobium leguminosarum bv. viciae 3841 NC_008380,NC_008382,NC_008383,NC_008379,NC_008381,NC_008384,NC_008378 1 6 legumes Plant/agriculture-associated 68192 Rhizobium sp. IRBG74 NC_022535.1,NC_022545.1,NC_022536.1 2 1 Plant/agriculture-associated 150571 Rhizobium tropici CIAT 899 NC_020059.1,NC_020060.1,NC_020061.1,NC_020062.1 1 3 common bean nodule but has a broad legume host range isolated from a common bean nodule but has a broad legume host range Plant/agriculture-associated 134200 Rhodobacter capsulatus SB 1003 NC_014034,NC_014035 1 1 the classical progenitor strain B10 isolated in the laboratory of Barry Marrs from the classical progenitor strain B10 Lab/Engineered 57909 Rhodobacter sphaeroides 2.4.1 NC_007493,NC_007494,NC_009007,NC_007488,NC_007489,NC_007490,NC_009008 2 5 type strain unknown 94549 Rhodobacter sphaeroides ATCC 17025 NC_009428,NC_009430,NC_009431,NC_009432,NC_009433,NC_009429 1 5 Wild-type strain of R. sphaeroides unknown 114483 Rhodobacter sphaeroides ATCC 17029 NC_009049,NC_009050,NC_009040 2 1 Wild-type strain of R. sphaeroides unknown 125910 Rhodobacter sphaeroides KD131 NC_011963,NC_011958,NC_011962,NC_011960 2 2 Sea mud off the coast of DaeBu Island, South Korea Aquatic-environment 141084 Rhodococcus equi 103S NC_014659 1 0 A prototypic Clinical/Human-associated isolate Clinical/Human-associated 231057 Rhodococcus erythropolis CCM2595 NC_022115.1,NC_022125.1 1 1 isolated from soil soil 66701 Rhodococcus erythropolis PR4 NC_012490,NC_007486,NC_007487,NC_007491 1 3 Pacific Ocean seawater isolated from Pacific Ocean seawater Aquatic-environment 26306 Rhodococcus jostii RHA1 NC_008268,NC_008269,NC_008270,NC_008271 1 3 soil contaminated with gamma-hexachlorocyclohexane (lindane: a toxic insecticide) isolated from soil contaminated with gamma-hexachlorocyclohexane (lindane: a toxic insecticide) in Japan Polluted/impacted environment 21106 Rhodococcus opacus B4 NC_012522,NC_006969,NC_012520,NC_012521,NC_012523,NC_006970 1 5 isolated from soil soil 320904 Rhodococcus pyridinivorans SB3094 NC_023150.1,NC_023145.1,NC_023144.1 1 2 isolated from a diesel waste site (Salem, VA) Polluted/impacted environment 131161 Rhodoferax ferrireducens T118 NC_007908,NC_007901 1 1 aquifer sediment collected at a depth of 18 feet isolated from aquifer sediment collected at a depth of 18 feet Aquatic-environment 113057 Rhodomicrobium vannielii ATCC 17100 NC_014664 1 0 unknown 59814 Rhodopirellula baltica SH 1 NC_005027 1 0 water column of Kieler Bucht (a fiord near the city of Kiel isolated from the water column of Kieler Bucht (a fiord near the city of Kiel in Germany) and seems to be strongly involved in the first part of the degradation of complex macromolecules produced by autotrophic organisms like algae and cyanobacteria Aquatic-environment 93214 Rhodopseudomonas palustris BisA53 NC_008435 1 0 freshwater sediment samples from De Biesbosch and Haren, the Netherlands Aquatic-environment 29154 Rhodopseudomonas palustris BisB18 NC_007925 1 0 freshwater sediment samples from De Biesbosch and Haren, the Netherlands Aquatic-environment 120395 Rhodopseudomonas palustris BisB5 NC_007958 1 0 freshwater sediment samples from De Biesbosch and Haren, the Netherlands Aquatic-environment 84835 Rhodopseudomonas palustris CGA009 NC_005296,NC_005297 1 1 chloramphenicol-resistant derivative of R palustris strain CGA001 Polluted/impacted environment 82507 Rhodopseudomonas palustris DX-1 NC_014834 1 0 microbial fuel cell Lab/Engineered 125544 Rhodopseudomonas palustris HaA2 NC_007778 1 0 freshwater sediments from De Biesbosch and Haren Aquatic-environment 88240 Rhodopseudomonas palustris TIE-1 NC_011004 1 0 iron-rich microbial mat from School Street Marsh isolated from an iron-rich microbial mat from School Street Marsh in Woods Hole, MA Extreme-environment 1465 Rhodospirillum centenum SW NC_011420 1 0 hot spring mud in Wyoming, United States Extreme-environment 237988 Rhodospirillum photometricum DSM122 NC_017059.1 1 0 unknown 82919 Rhodospirillum rubrum ATCC 11170 NC_007643,NC_007641 1 1 unknown 200464 Rhodospirillum rubrum F11 NC_017584 1 0 F11 is a mutant strain of Rhodospirillum rubrum (ATCC 11170) Lab/Engineered 93821 Rhodothermus marinus DSM 4252 NC_013501,NC_013502 1 1 shallow marine hot spring off the coast of Iceland isolated from a shallow marine hot spring off the coast of Iceland Extreme-environment 170506 Rhodothermus marinus SG0.5JP17-172 NC_015966,NC_015970,NC_015967 1 2 oil-contaminated soil Polluted/impacted environment 6986 Rickettsia africae ESF-5 NC_012633,NC_012634 1 1 cattle tick, Amblyomma variegatum, collected isolated from a cattle tick, Amblyomma variegatum, collected in Ethiopia and will be used for comparative genomics Insect-associated/other symbiont 50705 Rickettsia akari str. Hartford NC_009881 1 0 mites isolated from mites in Hartford and will be used for comparative analysis with other Rickettsia species Insect-associated/other symbiont 231019 Rickettsia australis str. Cutlack NC_017058.1,NC_017041.1 1 1 unknown 35792 Rickettsia bellii OSU 85-389 NC_009883 1 0 Isolated in Vero cell culture at 34 C by Karl Poetter and Chip Pretzman; spaghetti forms seen unknown 102610 Rickettsia bellii RML369-C NC_007940 1 0 triturated (powdered) pool of unfed adult Dermacentor variabilis ticks collected from vegetation near Fayetteville, Arkansas, USA, isolated in embryonated chicken eggs from a triturated (powdered) pool of unfed adult Dermacentor variabilis ticks collected from vegetation near Fayetteville, Arkansas, USA, in 1966 Insect-associated/other symbiont 238964 Rickettsia canadensis str. CA410 NC_016929.1 1 0 unknown 89738 Rickettsia canadensis str. McKiel NC_009879 1 0 ticks isolated from ticks in a field study on tick-transmitted diseases of small mammals in Canada Insect-associated/other symbiont 45613 Rickettsia conorii str. Malish 7 NC_003103 1 0 human isolated from a human in South Africa Clinical/Human-associated 64634 Rickettsia felis URRWXCal2 NC_007109,NC_007110,NC_007111 1 2 flea Insect-associated/other symbiont 193551 Rickettsia heilongjiangensis 054 NC_015866 1 0 isolated from Dysmicoccus sylvarum ticks in the Heilongjiang province of China in 1983 Insect-associated/other symbiont 83739 Rickettsia japonica YH NC_016050 1 0 "isolated in 1985 from the blood of a patient in Japan" Clinical/Human-associated 83254 Rickettsia massiliae MTU5 NC_009900,NC_009897 1 1 the tick Rhipicephalus turanicus collected from horses isolated from the tick Rhipicephalus turanicus collected from horses in Le Sambuc, Bouches-du Rhone, France Insect-associated/other symbiont 238520 Rickettsia massiliae str. AZT80 NC_016931.1,NC_016939.1 1 1 Clinical/Human-associated 232555 Rickettsia montanensis str. OSU 85-930 NC_017043.1 1 0 Clinical/Human-associated 233447 Rickettsia parkeri str. Portsmouth NC_017044.1 1 0 from a patient Clinical/Human-associated 48268 Rickettsia peacockii str. Rustic NC_012730,NC_012732 1 1 in a Rocky Mountain wood tick Insect-associated/other symbiont 124131 Rickettsia philipii str. 364D NC_016930.1 1 0 Insect-associated/other symbiont 89493 Rickettsia prowazekii Rp22 NC_017560 1 0 was isolated from a patient in 1999 Clinical/Human-associated 269054 Rickettsia prowazekii str. Breinl NC_020993.1 1 0 patients in Poland Clinical/Human-associated 229008 Rickettsia prowazekii str. BuV67-CWPP NC_017056.1 1 0 Clinical/Human-associated 240232 Rickettsia prowazekii str. Chernikova NC_017049.1 1 0 Clinical/Human-associated 238803 Rickettsia prowazekii str. Dachau NC_017051.1 1 0 Clinical/Human-associated 231244 Rickettsia prowazekii str. GvV257 NC_017048.1 1 0 Clinical/Human-associated 230392 Rickettsia prowazekii str. Katsinyian NC_017050.1 1 0 Clinical/Human-associated 72556 Rickettsia prowazekii str. Madrid E NC_000963 1 0 typhus patient isolated from a typhus patient in Madrid Clinical/Human-associated 275611 Rickettsia prowazekii str. NMRC Madrid E NC_020992.1 1 0 Clinical/Human-associated 237744 Rickettsia prowazekii str. RpGvF24 NC_017057.1 1 0 Clinical/Human-associated 233851 Rickettsia rhipicephali str. 3-7-female6-CWPP NC_017042.1,NC_017055.1 1 1 Clinical/Human-associated 236594 Rickettsia rickettsii str. Arizona NC_016909.1 1 0 Cell culture isolate from blood of a patient who died of RMSF Clinical/Human-associated 239281 Rickettsia rickettsii str. Brazil NC_016913.1 1 0 Possible yolk sac isolate (exact passage history unknown), presumably from a tick (exact history unknown) Insect-associated/other symbiont 228121 Rickettsia rickettsii str. Colombia NC_016908.1 1 0 Presumably yolk sac isolate (exact passage history unknown) from a patient suffering from RMSF Clinical/Human-associated 233768 Rickettsia rickettsii str. Hauke NC_016911.1 1 0 Cell culture isolate from lung tissue of a patient who died of RMSF Clinical/Human-associated 235723 Rickettsia rickettsii str. Hino NC_016914 1 0 Yolk sac isolate from a patient who died of RMSF Clinical/Human-associated 236174 Rickettsia rickettsii str. Hlp#2 NC_016915.1 1 0 Yolk sac isolate from H. leporispalustris tick Insect-associated/other symbiont 59104 Rickettsia rickettsii str. Iowa NC_010263 1 0 clonal isolate of R. rickettsii Iowa was derived from a single plaque from a high-egg-passage stock (EP 271) Lab/Engineered 5337 Rickettsia rickettsii str. 'Sheila Smith' NC_009882 1 0 from a patient with Rocky Mountain spotted fever isolated from from a patient with Rocky Mountain spotted fever and will be used for comparative analysis Clinical/Human-associated 180092 Rickettsia slovaca 13-B NC_016639 1 0 ticks throughout Europe isolated from ticks throughout Europe Insect-associated/other symbiont 233215 Rickettsia slovaca str. D-CWPP NC_017065.1 1 0 Insect-associated/other symbiont 187203 Rickettsia typhi str. B9991CWPP NC_017062.1 1 0 Bandicoot rats (Bandicota sp isolated from Bandicoot rats (Bandicota sp Terrestrial-animal-associated 188083 Rickettsia typhi str. TH1527 NC_017066.1 1 0 blood of a human with murine typhus isolated in April 1965 Thailand from blood of a human with murine typhus in the District Hospital in Chiang Rai Province, Thailand; This as the first case of murine typhus reported in Thailand Clinical/Human-associated 34752 Rickettsia typhi str. Wilmington NC_006142 1 0 blood from patient, North Carolina, 1928 Clinical/Human-associated 155424 Riemerella anatipestifer DSM 15868 NC_014738 1 0 isolated from blood of ducklings on Long Island, New York Terrestrial-animal-associated 258705 Riemerella anatipestifer RA-CH-1 NC_018609 1 0 sick duck sick ducks in the SiChuang province of China Terrestrial-animal-associated 270683 Riemerella anatipestifer RA-CH-2 NC_020125.1 1 0 sick ducks in the SiChuang province of China Terrestrial-animal-associated 184287 Riemerella anatipestifer RA-GD NC_017569 1 0 infected duck isolated from an infected duck Terrestrial-animal-associated 77222 Rivularia sp. PCC 7116 NC_019678.1,NC_019679.1,NC_019686.1 1 2 unialgal culture in marine water Lab/Engineered 55773 Robiginitalea biformata HTCC2501 NC_013222 1 0 Seawater taken at a depth of 10m from the Sargasso Sea Aquatic-environment 36679 Roseburia hominis A2-183 NC_015977 1 0 Human faecal sample Clinical/Human-associated 153491 Roseburia intestinalis M50/1 NC_021040 1 0 Clinical/Human-associated 152332 Roseburia intestinalis XB6B4 NC_021012 1 0 Clinical/Human-associated 91182 Roseiflexus castenholzii DSM 13941 NC_009767 1 0 hot spring microbial mat isolated from a hot spring microbial mat and will be used for comparative genomics with other phototrophic bacteria Extreme-environment 109359 Roseiflexus sp. RS-1 NC_009523 1 0 hot spring microbial mat isolated from a hot spring microbial mat Extreme-environment 86677 Roseobacter denitrificans OCh 114 NC_008209,NC_008386,NC_008387,NC_008388,NC_008389 1 4 seaweed, Enteromorpha linza Plant/agriculture-associated 160907 Rothia dentocariosa ATCC 17931 NC_014643 1 0 Human oral sample Clinical/Human-associated 152186 Rothia mucilaginosa NC_013715 1 0 A Clinical/Human-associated isolate Clinical/Human-associated 184445 Rubrivivax gelatinosus IL144 NC_017075.1 1 0 Japanese pond isolated from Japanese pond Aquatic-environment 52678 Rubrobacter xylanophilus DSM 9941 NC_008148 1 0 Thermally polluted industrial runoff from a carpet factory in Wilton, Wiltshire, UK Polluted/impacted environment 114501 Ruegeria pomeroyi DSS-3 NC_003911,NC_006569 1 1 isolated off of the coast of Georgia in 1998 Aquatic-environment 69653 Ruegeria sp. TM1040 NC_008044,NC_008043,NC_008042 1 2 culture of the dinoflagellate Pfiesteria piscicida CCMP1830 which has been implicated isolated from a culture of the dinoflagellate Pfiesteria piscicida CCMP1830 which has been implicated in many large scale algal blooms resulting in increased mortality in fish Polluted/impacted environment 150544 Ruminococcus albus 7 NC_014826,NC_014833,NC_014827,NC_014824,NC_014825 1 4 Bovine rumen Terrestrial-animal-associated 49525 Ruminococcus bromii L2-63 NC_021013 1 0 Human feces from Rowett Research Institute, Aberdeen Clinical/Human-associated 55702 Ruminococcus champanellensis 18P13 NC_021039 1 0 human intestine (feces) Cellulolytic bacterium from the human intestine Clinical/Human-associated 156199 Ruminococcus obeum A2-162 NC_021022 1 0 Clinical/Human-associated 156992 Ruminococcus sp. SR1/5 NC_021014 1 0 Human feces Clinical/Human-associated 148568 Ruminococcus torques L2-14 NC_021015 1 0 Clinical/Human-associated 161982 Runella slithyformis DSM 19594 NC_015703,NC_015693,NC_015704,NC_015694,NC_015705,NC_015695 1 5 Fresh water lake Aquatic-environment 111818 Saccharomonospora viridis DSM 43017 NC_013159 1 0 Irish peat and was originally classified as Thermomonospora viridis isolated from Irish peat and was originally classified as Thermomonospora viridis Plant/agriculture-associated 56404 Saccharophagus degradans 2-40 NC_007912 1 0 decaying Spartina alterniflora, a salt marsh cord grass, isolated from decaying Spartina alterniflora, a salt marsh cord grass, in the Chesapeake Bay, USA Plant/agriculture-associated 28377 Saccharopolyspora erythraea NRRL 2338 NC_009142 1 0 soil, Philippines soil 246561 Saccharothrix espanaensis DSM 44229 NC_019673.1 1 0 was obtained as lyophilized culture from DSMZ (Braunschweig, Germany) unknown 86502 Salinibacter ruber DSM 13855 NC_007677,NC_007678 1 1 Saltern crystallizer ponds in Spain Extreme-environment 49863 Salinibacter ruber M8 NC_014032.1,NC_014030,NC_014028,NC_014026,NC_014157 1 4 isolated in September 1999 from a Mediterranean solar saltern. Extreme-environment 38676 Salinispora arenicola CNS-205 NC_009953 1 0 Beach sand at a depth of 1 meter from Sweetings Cay in the Bahamas Aquatic-environment 43511 Salinispora tropica CNB-440 NC_009380 1 0 coarse beach sand off the Bahamas, isolated from coarse beach sand off the Bahamas, and is being sequenced for comparative genome analysis Aquatic-environment 251618 Salmonella bongori N268-08 NC_021870.1,NC_021871.1 1 1 a Clinical/Human-associated isolate from Switzerland Clinical/Human-associated 28203 Salmonella bongori NCTC 12419 NC_015761 1 0 originally isolated from an African frog in 1972 (Salmonella Reference Collection C strain SARC11) Terrestrial-animal-associated 13497 Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- str. RSK2980 NC_010067 1 0 cornsnake isolated from a cornsnake in 1986 in Oregon Terrestrial-animal-associated 301979 Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. 08-1736 NC_021820.1 1 0 unknown Salmonella enterica subsp. enterica serovar Agona 24249 NC_022991 1 0 sourced directly from the food factory food-associated 65316 Salmonella enterica subsp. enterica serovar Agona str. SL483 NC_011149,NC_011148 1 1 from human sources as reported by the CDC Clinical/Human-associated 280277 Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000189 NC_021844.1,NC_021817.1 1 1 Shrimp, Frozen Raw Food-associated 314241 Salmonella enterica subsp. enterica serovar Bovismorbificans str. 3114 NC_022241,NC_022248 1 0 isolate from Malawi, was sequenced Terrestrial-animal-associated 136302 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 NC_006905,NC_006855,NC_006856 1 2 58-year old man with sepsis and has been shown to be resistant to ciprofloxacin and ceftriaxone isolated from a 58-year old man with sepsis and has been shown to be resistant to ciprofloxacin and ceftriaxone Clinical/Human-associated 305815 Salmonella enterica subsp. enterica serovar Cubana str. CFSAN002050 NC_021818.1,NC_021845.1,NC_021819.1 1 2 Fresh alfalfa sprouts Plant/agriculture-associated 111443 Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853 NC_011205,NC_011204 1 1 cattle Terrestrial-animal-associated 14964 Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 NC_011294 1 0 isolated from an outbreak of human food-poisoning in the United Kingdom Clinical/Human-associated 1629 Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 NC_011274 1 0 isolated from an outbreak of fowl typhoid in brown egg–laying hens Terrestrial-animal-associated Salmonella enterica subsp. enterica serovar Gallinarum/pullorum CDC1983-67 NC_022221 1 0 Terrestrial-animal-associated Salmonella enterica subsp. enterica serovar Gallinarum/pullorum str. RKS5078 NC_016831 1 0 chicken-addpated Terrestrial-animal-associated 230047 Salmonella enterica subsp. enterica serovar Heidelberg str. 41578 NC_021810.1,NC_021869.1,NC_021841.1,NC_021811.1 1 3 Stool from human sources as reported by the CDC Clinical/Human-associated 231328 Salmonella enterica subsp. enterica serovar Heidelberg str. B182 NC_017623.1,NC_017624.1 1 1 isolated from bovine feces (France) Terrestrial-animal-associated 300642 Salmonella enterica subsp. enterica serovar Heidelberg str. CFSAN002069 NC_021812.1,NC_021842.1,NC_021813.1 1 2 Chicken Terrestrial-animal-associated 43179 Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 NC_011083,NC_011082,NC_011081 1 2 Isolated from ground turkey in Minnesota in 2003. Terrestrial-animal-associated 282587 Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992 NC_020307.1,NC_020306.1,NC_020308.1 1 2 Stool from human sources as reported by the CDC Clinical/Human-associated 114557 Salmonella enterica subsp. enterica serovar Newport str. SL254 NC_011080,NC_011079,NC_009140 1 2 Isolated from a human in Minnesota in 2000. from human sources as reported by the CDC Clinical/Human-associated 166060 Salmonella enterica subsp. enterica serovar Newport str. USMARC-S3124.1 NC_021902.1 1 0 Terrestrial-animal-associated 134303 Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601 NC_011147 1 0 child with paratyphoid fever This strain is a Clinical/Human-associated isolate collected from a child with paratyphoid fever in Karachi, Pakistan, 2004 Clinical/Human-associated 134188 Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 NC_006511 1 0 Paratyphoid fever Clinical/Human-associated 120821 Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7 NC_010102 1 0 stool sample isolated by Kwai-Lin Thong. Isolated from the stool of a female in Penang Malaysia. Clinical/Human-associated 12305 Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594 NC_012125,NC_012124 1 1 Isolated from man in France in 1988. Clinical/Human-associated 284818 Salmonella enterica subsp. enterica serovar Pullorum str. S06004 NC_021984.1 1 0 unknown 87589 Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633 NC_011094,NC_011093,NC_011092 1 2 Isolated from dehydrated chili in Thailand in 2002. Plant/agriculture-associated 228911 Salmonella enterica subsp. enterica serovar Thompson str. RM6836 NC_022525.1 1 0 isolated from lettuce in 2002 Plant/agriculture-associated 120419 Salmonella enterica subsp. enterica serovar Typhi str. CT18 NC_003198,NC_003384,NC_003385 1 2 isolated from blood Isolated in December 1993 at the Mekong Delta region of Vietnam, from blood of a 9-year-old girl who was suffering from typhoid. Clinical/Human-associated 217276 Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12 NC_016832,NC_016825 1 1 Typhoid Carrier isolate obtained from a Typhoid Carrier in India Clinical/Human-associated 47697 Salmonella enterica subsp. enterica serovar Typhi str. Ty2 NC_004631 1 0 obtained from K. Sanderson (Salmonella Genetic Stock Center isolate 2666 isolated in the early 1970s, Isolated before the emergence of drug resistance in the 1970s. Clinical/Human-associated 53573 Salmonella enterica subsp. enterica serovar Typhi str. Ty21a NC_021176.1 1 0 the virulent S derived from the virulent S. typhi strain Ty2 by chemical (NTG) mutagenesis Lab/Engineered 111430 Salmonella enterica subsp. enterica serovar Typhimurium NC_016854 1 0 Isolated from the blood of a Malawian 26-mo-old child with malaria and anemia admitted to QECH in Blantyre, Malawi, in January 2004. isolated in 2004, at the peak of a Blantyre multidrug-resistant (MDR), invasive NTS epidemic Clinical/Human-associated 101322 Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S NC_016856,NC_016855 1 1 a descendant of CDC 60-6516, a strain isolated in 1960 from pools of hearts and livers of 4-week-old chickens Terrestrial-animal-associated 188007 Salmonella enterica subsp. enterica serovar Typhimurium str. 798 NC_017046.1,NC_017054.1 1 1 wild type from a pig Terrestrial-animal-associated 102764 Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 NC_022569.1,NC_022570.1 2 0 Terrestrial-animal-associated 94139 Salmonella enterica subsp. enterica serovar Typhimurium str. DT2 NC_022544.1 1 0 chicken Terrestrial-animal-associated 20916 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 NC_003197,NC_003277 1 1 isolated in the 1940s by Lilleengen, and typed based on phage sensitivity Clinical/Human-associated 88447 Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 NC_016810,NC_017718,NC_017719,NC_017720 1 3 The ancestral strain ST4/74 was originally isolated from the bowel of a calf with Salmonellosis (17) and used by Bruce Stocker to generate a histidine auxotroph named SL1344 Lab/Engineered 171491 Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 NC_016857,NC_016858,NC_017675,NC_016859 1 3 isolated from the bowel of a calf with Salmonellosis, UK Terrestrial-animal-associated 148416 Salmonella enterica subsp. enterica serovar Typhimurium str. T000240 NC_016860,NC_016861,NC_016862 1 2 Isolated from human gastroenteritis in 2000 in Japan. Clinical/Human-associated 235020 Salmonella enterica subsp. enterica serovar Typhimurium str. U288 NC_021151.1,NC_021156.1,NC_021155.1,NC_021157.1 1 3 pig production- related Terrestrial-animal-associated 184625 Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1 NC_016863,NC_016864 1 1 Isolated from the spleen of a chick orally inoculated 3 days earlier with a highly virulent S. Typhimurium strain retrieved from an infected horse in 1991. Terrestrial-animal-associated 317872 Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921 NC_021814.1,NC_021815.1,NC_021816.1,NC_021843.1 1 3 chicken breast Food-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187076 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187072 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187081 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187084 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187091 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187100 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187102 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187103 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187106 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187114 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187115 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187117 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187118 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187120 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187124 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187126 1 0 fresh-vegetable isolate Plant/agriculture-associated Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1 NT_187130 1 0 fresh-vegetable isolate Plant/agriculture-associated 123513 Sanguibacter keddieii DSM 10542 NC_013521 1 0 bovine blood isolated from bovine blood Terrestrial-animal-associated 202527 Saprospira grandis str. Lewin NC_016940.1,NC_016936.1 1 1 La Jolla beach Aquatic-environment 81212 Sebaldella termitidis ATCC 33386 NC_013517,NC_013519,NC_013518 1 2 posterior intestinal content of termites Insect-associated/other symbiont 244873 secondary endosymbiont of Ctenarytaina eucalypti Thao2000 NC_018419.1 1 0 psyllids Insect-associated/other symbiont 14126 secondary endosymbiont of Heteropsylla cubana Thao2000 NC_018420.1 1 0 psyllids Insect-associated/other symbiont 51051 Segniliparus rotundus DSM 44985 NC_014168 1 0 human sputum isolated from human sputum Clinical/Human-associated 203744 Selenomonas sputigena ATCC 35185 NC_015437 1 0 Subgingival sulcus Clinical/Human-associated 298176 Serratia liquefaciens ATCC 27592 NC_021741.1,NC_021742.1 1 1 was obtained from the American Type Culture Collection (Manassas, VA) unknown 265383 Serratia marcescens FGI94 NC_020064.1 1 0 isolated from a fungus garden of the leaf-cutter ant Atta colombica Insect-associated/other symbiont 101006 Serratia marcescens WW4 NC_020211.1,NC_020212.1 1 1 waste water of paper machine isolated from waste water of paper machine Polluted/impacted environment Serratia plymuthica 4Rx13 NC_021591,NC_021594 1 1 found in human clinical specimens and in food. food-associated 291149 Serratia plymuthica S13 NC_021659.1 1 0 Styrian pumpkin anthrosphere Plant/agriculture-associated 44537 Serratia proteamaculans 568 NC_009832,NC_009829 1 1 Root endophyte from Populus trichocarpa Plant/agriculture-associated 169681 Serratia sp. AS12 NC_015566 1 0 Rapeseed plant roots Plant/agriculture-associated 179563 Serratia sp. AS13 NC_017573 1 0 Rapeseed plant Plant/agriculture-associated 170685 Serratia sp. AS9 NC_015567 1 0 rapeseed roots and rhizosphere soils from Uppsala, Sweden Plant/agriculture-associated 8482 Serratia sp. ATCC 39006 NC_022268 1 0 channel water Aquatic-environment 87276 Serratia symbiotica str. 'Cinara cedri' NC_016632 1 0 Insect-associated/other symbiont 74963 Shewanella amazonensis SB2B NC_008700 1 0 shallow marine deposits (coastal shelf mud) of the Amazon River delta off of the coast of Brazil isolated from shallow marine deposits (coastal shelf mud) of the Amazon River delta off of the coast of Brazil Aquatic-environment 163160 Shewanella baltica OS117 NC_017579,NC_017577,NC_017580,NC_017578 1 3 Seawater from the oxygenated zone just above the chemocline (80 m), Gotland Deep, Baltic Sea Aquatic-environment 55297 Shewanella baltica OS155 NC_009052,NC_009036,NC_009037,NC_009038,NC_009035 1 4 the Baltic Sea isolated from the Baltic Sea Aquatic-environment 127872 Shewanella baltica OS185 NC_009665,NC_009661 1 1 sea-water; oxic-anoxic interface; 120 m depth from the Baltic Sea Aquatic-environment 33754 Shewanella baltica OS195 NC_009997,NC_009999,NC_010000,NC_009998 1 3 the Baltic Sea isolated from the Baltic Sea and will be used for comparative analysis Aquatic-environment 125792 Shewanella baltica OS223 NC_011663,NC_011668,NC_011665,NC_011664 1 3 Sea water, oxic-anoxic interface, 120m depth from the Baltic Sea Aquatic-environment 147952 Shewanella baltica OS678 NC_016901,NC_016905 1 1 Isolated from seawater from the low-oxygen zone just above the chemocline (110 m), Baltic Sea. Aquatic-environment 79529 Shewanella denitrificans OS217 NC_007954 1 0 the Gotland Deep, an anoxic basin isolated from the Gotland Deep, an anoxic basin in the central Baltic Sea in 1986 from a depth of 120-130 m (Gotland Deep: BY 15, 57-1920 degrees N, 20-0302 degrees E) Aquatic-environment 14343 Shewanella frigidimarina NCIMB 400 NC_008345 1 0 the North Sea near Aberdeen, United Kingdom isolated from the North Sea near Aberdeen, United Kingdom Aquatic-environment 24697 Shewanella halifaxensis HAW-EB4 NC_010334 1 0 sediment isolated from sediment in a munitions-dumping area of the Emerald Basin (depth of 215 m, Atlantic Ocean), offshore of Halifax Harbour (Nova Scotia, Canada) Aquatic-environment 132094 Shewanella loihica PV-4 NC_009092 1 0 the Naha Vents, Hawaii, in the Pacific Ocean isolate from the Naha Vents, Hawaii, in the Pacific Ocean Aquatic-environment 101494 Shewanella oneidensis MR-1 NC_004347,NC_004349 1 1 Oneida lake isolated from Oneida lake in New York, USA Aquatic-environment 72822 Shewanella pealeana ATCC 700345 NC_009901 1 0 Microbial community colonizing the accessory nidamental gland of the squid Loligo pealei, from Woods Hole Harbor, Massachusetts Aquatic-life-associated 65056 Shewanella piezotolerans WP3 NC_011566 1 0 Sediment; under 1,914 m of water depth collected in the west Pacific Ocean Aquatic-environment 89411 Shewanella putrefaciens 200 NC_017566 1 0 Canadian oil pipeline isolated from a Canadian oil pipeline Extreme-environment 135485 Shewanella putrefaciens CN-32 NC_009438 1 0 Subsurface; shale sandstone; 250 m depth from Albuquerque, New Mexico Aquatic-environment 62411 Shewanella sediminis HAW-EB3 NC_009831 1 0 Sediment at depth of 215m from an unexploded-ordinance-dumping site at Halifax Aquatic-environment 134792 Shewanella sp. ANA-3 NC_008573,NC_008577 1 1 arsenate treated wood pier that was isolated from an arsenate treated wood pier that was in a brackish estuary (Eel Pond) in Woods Hole, Massachusetts Polluted/impacted environment Shewanella sp. ANA-3 NC_008577,NC_008573 1 1 Arsenate treated wood pier that was in a brackish estuary (Eel Pond) in Woods Hole Massachusetts Polluted/impacted environment 133532 Shewanella sp. MR-4 NC_008321 1 0 the Black Sea isolate from the Black Sea Aquatic-environment 85603 Shewanella sp. MR-7 NC_008322,NC_008320 1 1 the Black Sea isolate from the Black Sea Aquatic-environment 103602 Shewanella sp. W3-18-1 NC_008750 1 0 marine sediments at a depth of 630 m. This strain was isolated from Pacific Ocean marine sediments at a depth of 630 m. Aquatic-environment 92117 Shewanella violacea DSS12 NC_014012 1 0 mud, taken at a depth of 5110 m, from the Ryukyu Trench isolated from mud, taken at a depth of 5110 m, from the Ryukyu Trench in the Philippine Sea Aquatic-environment 126588 Shewanella woodyi ATCC 51908 NC_010506 1 0 squid ink and seawater from depths of 200 to 300 m in the Alboran Sea Aquatic-environment 129590 Shigella boydii CDC 3083-94 NC_010658,NC_010657,NC_010659,NC_010660,NC_010672,NC_010656 1 5 12-year-old boy isolated from a 12-year-old boy in Arizona by Dr Nancy Stockbine Clinical/Human-associated 33460 Shigella boydii Sb227 NC_007613,NC_007608 1 1 epidemic in China in the 1950s isolate from an epidemic that took place in China in the 1950s Clinical/Human-associated 99784 Shigella dysenteriae Sd197 NC_007606,NC_009344,NC_007607 1 2 epidemic in China in the 1950s isolate from an epidemic in China in the 1950s Clinical/Human-associated 60233 Shigella flexneri 2002017 NC_017328,NC_017319,NC_017320,NC_017329,NC_017321,NC_017330 1 5 obtained from a 2-year-old patient in 2002 in Henan Province Clinical/Human-associated 31049 Shigella flexneri 2a str. 2457T NC_004741 1 0 human feces Clinical/Human-associated 86970 Shigella flexneri 2a str. 301 NC_004337,NC_004851 1 1 patient isolated in 1984 from a patient in Beijing, China Clinical/Human-associated 33408 Shigella flexneri 5 str. 8401 NC_008258 1 0 isolated and sequenced from epidemic in China Clinical/Human-associated Shigella sonnei 53G NC_016822,NC_016823,NC_016824,NC_016833,NC_016834 1 0 Shigellosis, human pathogen Isolated from 5 year old patient in Japan Clinical/Human-associated 107113 Shigella sonnei Ss046 NC_007384,NC_007385,NC_009345,NC_009346,NC_009347 1 4 epidemic in China in the 1950s isolate from an epidemic in China in the 1950s Clinical/Human-associated 78014 Shimwellia blattae DSM 4481 NC_017910.1 1 0 isolated from a cockroach Insect-associated/other symbiont 69165 Sideroxydans lithotrophicus ES-1 NC_013959 1 0 iron contaminated groundwater in Michigan Polluted/impacted environment 223159 Simiduia agarivorans SA1 = DSM 21679 NC_018868 1 0 Isolated from shallow coastal seawater. Coastal region of Keelung Aquatic-environment 162252 Simkania negevensis Z NC_015710,NC_015713 1 1 contaminated Vero cells passaged in Israel Polluted/impacted environment 225422 Sinorhizobium fredii NC_016812.1,NC_016814.1,NC_016815.1,NC_016836.1,NC_016813.1 1 4 isolated from Chinese soil associated to soybean from Hubei Province Plant/agriculture-associated 122450 Sinorhizobium fredii NGR234 NC_012587,NC_000914,NC_012586 1 2 Plant/agriculture-associated 247491 Sinorhizobium fredii USDA 257 NC_018000,NT_187163,NT_187151,NT_187152,NT_187164,NT_187153,NT_187154,NT_187165,NT_187155,NT_187166,NT_187156,NT_187157,NT_187167,NT_187158,NT_187159,NT_187168,NT_187160,NT_187162,NT_187161,NT_187169 1 18 wild soybean roots collected isolated from wild soybean roots collected in China and has an extremely broad host range (79 legume plant genera) Plant/agriculture-associated 134228 Sinorhizobium medicae WSM419 NC_009636,NC_009621,NC_009622,NC_009620 1 3 isolated from a M. murex root nodule collected in Sardinia, Italy in 1981 Plant/agriculture-associated 96828 Sinorhizobium meliloti 1021 NC_003047,NC_003037,NC_003078 1 2 Plant/agriculture-associated 287203 Sinorhizobium meliloti 2011 NC_020528.1,NC_020560.1,NC_020527.1 1 2 Plant/agriculture-associated 272116 Sinorhizobium meliloti GR4 NC_019845.1 1 0 agricultural field Plant/agriculture-associated 255716 Sinorhizobium meliloti Rm41 NC_018700.1,NC_018683.1,NC_018701.1,NC_018682.1 1 3 root nodules of Melilotus and Medicago Plant/agriculture-associated 152503 Sinorhizobium meliloti SM11 NC_017325,NC_017327,NC_017326 1 2 isolated from a root nodule of an alfalfa plant, grown in a field plot in Strassmoos (Bavaria, Germany) Plant/agriculture-associated 66389 Slackia heliotrinireducens DSM 20476 NC_013165 1 0 Sheep rumen, Australia Terrestrial-animal-associated 61428 Sodalis glossinidius str. 'morsitans' NC_007712,NC_007713,NC_007714,NC_007715 1 3 Isolated from secondary symbiont of Glossina morsitans morsitans Insect-associated/other symbiont 188029 Solibacillus silvestris StLB046 NC_018065.1,NC_018069.1 1 1 potato leaf collected in Minamishimabara, Nagasaki, Japan Plant/agriculture-associated 80414 Sorangium cellulosum 'So ce 56' NC_010162 1 0 biotechnological importance Isolated from a soil sample containing decaying plant material in Indonesia in 1985. soil 270250 Sorangium cellulosum So0157-2 NC_021658.1 1 0 an alkaline soil sample Extreme-environment 120955 Sphaerobacter thermophilus DSM 20745 NC_013523,NC_013524 2 0 aerobic thermophilic sewage sludge isolated from aerobic thermophilic sewage sludge Polluted/impacted environment 156491 Sphaerochaeta coccoides DSM 17374 NC_015436 1 0 Hindgut of the termite Neotermes castaneus; Cuba Insect-associated/other symbiont 118584 Sphaerochaeta pleomorpha str. Grapes NC_016633 1 0 black, anoxic river sediments downstream of an agricultural and residential area Polluted/impacted environment 132844 Sphaerochaeta sp. Buddy NC_015152 1 0 black, anoxic river sediments downstream of an agricultural and residential area Polluted/impacted environment 165585 Sphingobacterium sp. 21 NC_015277 1 0 Compost Feedstock-Adapted Isolate Polluted/impacted environment 147895 Sphingobium japonicum UT26S NC_014006,NC_014009,NC_014013,NC_014005,NC_014007 2 3 upland γ-HCH contaminated soil in Japan Polluted/impacted environment 26123 Sphingobium sp. SYK-6 NC_015976,NC_015974 2 0 waste liquor of a kraft pulp mill Polluted/impacted environment 55028 Sphingomonas wittichii RW1 NC_009511,NC_009508,NC_009507 1 2 Elbe River in Germany Elbe River, downstream Hamburg harbour Polluted/impacted environment 23391 Sphingopyxis alaskensis RB2256 NC_008048,NC_008036 1 1 Resurrection Bay isolated from Resurrection Bay in the Gulf of Alaska Aquatic-environment 269535 Spiribacter salinus M19-40 NC_021291.1 1 0 solar saltern of 19% salinity isolated from a Spanish saltern of intermediate salinity Extreme-environment 312729 Spiribacter sp. UAH-SP71 NC_022664.1 1 0 solar saltern isolated from a solar saltern Extreme-environment 172053 Spirochaeta africana DSM 8902 NC_017098.1 1 0 Bacterial bloom in the brine under trona from alkaline equatorial Lake Magadi in Kenya Extreme-environment 89994 Spirochaeta smaragdinae DSM 11293 NC_014364 1 0 Oil field of Congo, Africa Extreme-environment 282895 Spirochaeta sp. L21-RPul-D2 NC_023035 1 0 mineralizing microbial mat of the hypersaline Lake 21 on the Kiritimati Atoll Extreme-environment 146732 Spirochaeta thermophila DSM 6192 NC_014484 1 0 Brackish hot spring on Raoul Island, New Zealand Extreme-environment 268198 Spiroplasma apis B31 NC_022998.1 1 0 Insect France Insect-associated/other symbiont 270872 Spiroplasma chrysopicola DF-1 NC_021280.1 1 0 deer fly gut, Chrysops sp., Beltsville, MD [23674] Insect-associated/other symbiont 276024 Spiroplasma diminutum CUAS-1 NC_021833.1 1 0 Mosquito, Culex annulus, Taiwan Insect-associated/other symbiont 267119 Spiroplasma syrphidicola EA-1 NC_021284.1 1 0 Syrphid fly, Eristalis arbustorum, Beltsville, MD Insect-associated/other symbiont 276134 Spiroplasma taiwanense CT-1 NC_021846.1,NC_021832.1 1 1 mosquito, Culex tritaeniorhynchus, Taiwan Insect-associated/other symbiont 97822 Spirosoma linguale DSM 74 NC_013730,NC_013732,NC_013733,NC_013734,NC_013735,NC_013736,NC_013737,NC_013738,NC_013731 1 8 laboratory water bath isolated from a laboratory water bath Lab/Engineered 43420 Stackebrandtia nassauensis DSM 44728 NC_013947 1 0 roadside soil sample collected from a roadside soil sample in Nassau, Bahamas soil 5387 Stanieria cyanosphaera PCC 7437 NC_019748.1,NC_019765.1,NC_019749.1,NC_019766.1,NC_019750.1,NC_020052.1 1 5 pool at botanical garden Aquatic-environment 158479 Staphylococcus aureus 04-02981 NC_017340 1 0 Isolated in Koeln, Germany in 2004. Clinical/Human-associated 253481 Staphylococcus aureus 08BA02176 NC_018608.1 1 0 soft tissue infection of skin Clinical/Human-associated 297053 Staphylococcus aureus Bmb9393 NC_021670.1,NC_021657.1 1 1 patient with blood stream infection isolated from a patient with blood stream infection in a hospital located in Rio de Janeiro, Brazil in 1993 Clinical/Human-associated 292900 Staphylococcus aureus CA-347 NC_021554.1,NC_021552.1 1 1 from a bacteremia infection in 2005 in California Clinical/Human-associated 280917 Staphylococcus aureus M1 NC_021059.1,NC_021060.1 1 1 This Clinical/Human-associated isolate was from the index patient of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in Copenhagen, Denmark, that started in 2003 Clinical/Human-associated 92441 Staphylococcus aureus RF122 NC_007622 1 0 cow presenting with clinical mastitis in 1993 Terrestrial-animal-associated 227088 Staphylococcus aureus ST228/10388 NC_020529.1,NC_020530.1 1 1 in a tertiary care of Lausanne hospital Clinical/Human-associated 231791 Staphylococcus aureus ST228/10497 NC_020564.1,NC_020531.1 1 1 in a tertiary care of Lausanne hospital Clinical/Human-associated 229824 Staphylococcus aureus ST228/15532 NC_020532.1,NC_020565.1 1 1 in a tertiary care of Lausanne hospital Clinical/Human-associated 227615 Staphylococcus aureus ST228/16035 NC_020533.1,NC_020534.1 1 1 in a tertiary care of Lausanne hospital Clinical/Human-associated Staphylococcus aureus ST228/16125 NC_020566, NC_020535 1 1 in a tertiary care hospital. Clinical/Human-associated Staphylococcus aureus ST228/18341 NC_020536,NC_020567 1 1 in a tertiary care hospital. Clinical/Human-associated 233200 Staphylococcus aureus ST228/18412 NC_020537.1,NC_020538.1 1 1 in a tertiary care of Lausanne hospital Clinical/Human-associated Staphylococcus aureus ST228/18583 NC_020568,NC_020539 1 1 in a tertiary care hospital. Clinical/Human-associated 217024 Staphylococcus aureus subsp. aureus 11819-97 NC_017351,NC_017350 1 1 skin abscess Danish Clinical/Human-associated MRSA isolate, collected from a skin abscess Clinical/Human-associated Staphylococcus aureus subsp. aureus 55/2053 NC_022113,NC_022126 1 1 Clinical/Human-associated 307966 Staphylococcus aureus subsp. aureus 6850 NC_022222.1 1 0 patient with a complicated S derived from a patient with a complicated S. aureus bacteremia, associated with osteomyelitis and septic arthritis Clinical/Human-associated 238986 Staphylococcus aureus subsp. aureus 71193 NC_017673.1 1 0 The first ST398 MSSA strain isolated in 2004, designated 71193 or ST398NM01 Clinical/Human-associated 249160 Staphylococcus aureus subsp. aureus CN1 NC_022226.1,NC_022228.1,NC_022227.1 1 2 Korea from the pus of a necrotizing fasciitis infection in an 80-year old patient in the Seoul area of South Korea Clinical/Human-associated 112458 Staphylococcus aureus subsp. aureus COL NC_002951,NC_006629 1 1 Isolated as a penicillinase-negative strain in the early 1960s from the operating theatre in a hospital in Colindale, England Clinical/Human-associated 171735 Staphylococcus aureus subsp. aureus ECT-R 2 NC_017343,NC_017346,NC_017344 1 2 human wound secretion Clinical/Human-associated 142340 Staphylococcus aureus subsp. aureus ED133 NC_017337 1 0 ruminant isolate Terrestrial-animal-associated 139507 Staphylococcus aureus subsp. aureus ED98 NC_013450,NC_013452,NC_013453,NC_013451 1 3 broiler chicken isolated from a broiler chicken in Northern Ireland Terrestrial-animal-associated 229418 Staphylococcus aureus subsp. aureus HO 5096 0412 NC_017763.1 1 0 isolates both from hospital and community settings Clinical/Human-associated 98826 Staphylococcus aureus subsp. aureus JH1 NC_009632,NC_009619 1 1 patient undergoing vancomycin treatment isolated from a patient undergoing vancomycin treatment Clinical/Human-associated 42398 Staphylococcus aureus subsp. aureus JH9 NC_009487,NC_009477 1 1 patient undergoing vancomycin treatment isolated from a patient undergoing vancomycin treatment Clinical/Human-associated 164993 Staphylococcus aureus subsp. aureus JKD6159 NC_017338,NC_017339 1 1 Clinical/Human-associated isolate isolated from a pure culture of the bacteriumThis is the first complete genome for methicillin resistance Staphylococcus aureus (MRSA) clone ST93 Clinical/Human-associated 208671 Staphylococcus aureus subsp. aureus LGA251 NC_017349,NC_017348 1 1 isolated from a bulk milk sample from a farm in southwest England in May, 2007 Terrestrial-animal-associated 221819 Staphylococcus aureus subsp. aureus M013 NC_016928 1 0 wound specimen from a pediatric outpatient Isolated in 2002 from a wound specimen of a pediatric outpatient during part of the Taiwan Surveillance of Antimicrobial Resistance surveillance (TSAR) project. Clinical/Human-associated 71814 Staphylococcus aureus subsp. aureus MRSA252 NC_002952 1 0 hospital-acquired This strain is a hospital-acquired strain isolated in the United Kingdom, representative of the methicillin-resistant (MRSA) strains Clinical/Human-associated 224518 Staphylococcus aureus subsp. aureus MSHR1132 NC_016941.1,NC_016942.1 1 0 blood culture of an indigenous woman with necrotizing fasciitis at the Royal Darwin Hospital (RDH), Darwin, Northern Territory, Australia Clinical/Human-associated 96780 Staphylococcus aureus subsp. aureus MSSA476 NC_002953,NC_005951 1 1 community acquired This strain is a hyper-virulent community acquired methicillin-susceptible (MSSA) strain isolated in the United Kingdom. Clinical/Human-associated 127830 Staphylococcus aureus subsp. aureus Mu3 NC_009782 1 0 sputum from a lung cancer patient with MRSA pneumonia, Japan Clinical/Human-associated 52173 Staphylococcus aureus subsp. aureus Mu50 NC_002758,NC_002774 1 1 the pus of a Japanese male baby with a surgical wound infection that did not respond to vancomycin isolated in 1997 from the pus of a Japanese male baby with a surgical wound infection that did not respond to vancomycin Clinical/Human-associated 44266 Staphylococcus aureus subsp. aureus MW2 NC_003923 1 0 community acquired This strain is a community-acquired methicillin-resistant (MSRA) strain Clinical/Human-associated 116463 Staphylococcus aureus subsp. aureus N315 NC_002745,NC_003140 1 1 pharyngeal smear of a Japanese patient isolated in 1982 from a pharyngeal smear of a Japanese patient Clinical/Human-associated 99865 Staphylococcus aureus subsp. aureus NCTC 8325 NC_007795 1 0 SA113 R- m+ Plasmid host Clinical/Human-associated 247535 Staphylococcus aureus subsp. aureus SA40 NC_022443.1 1 0 Clinical/Human-associated 244664 Staphylococcus aureus subsp. aureus SA957 NC_022442.1 1 0 Clinical/Human-associated 143048 Staphylococcus aureus subsp. aureus ST398 NC_017333, NC_017334,NC_017335,NC_017336 1 3 Obtained in 2006 from a blood culture of a 63 year old female patient with endocarditis of the mitral valve. from a case of human endocarditis Clinical/Human-associated 110820 Staphylococcus aureus subsp. aureus str. JKD6008 NC_017341 1 0 Isolated from the bloodstream of a patient in New Zealand in 2003. A Clinical/Human-associated isolate of Staphylococcus aureus which is resistant to methicillin and has intermediate sensitivity to vancomycin. Clinical/Human-associated 133992 Staphylococcus aureus subsp. aureus str. Newman NC_009641 1 0 Human infection 1952 Clinical/Human-associated 188048 Staphylococcus aureus subsp. aureus T0131 NC_017347 1 0 87-year-old patient isolated in 2006, was recovered from an 87-year-old patient in No Clinical/Human-associated 17688 Staphylococcus aureus subsp. aureus TCH60 NC_017342,NC_017345 1 1 Human skin sample Clinical/Human-associated 147706 Staphylococcus aureus subsp. aureus TW20 NC_017331,NC_017352,NC_017332 1 2 Human and animal respiratory tract Clinical/Human-associated 129981 Staphylococcus aureus subsp. aureus USA300_FPR3757 NC_007793,NC_007790,NC_007791,NC_007792 1 3 Clinical/Human-associated 36919 Staphylococcus aureus subsp. aureus USA300_TCH1516 NC_010079,NC_012417,NC_010063 1 2 isolated at Texas Children's Hospital in Houston methicillin resistant strain Clinical/Human-associated 189714 Staphylococcus aureus subsp. aureus VC40 NC_016912 1 0 generated by serial passage of S. aureus RN4220ΔmutS, a mutS gene deletion mutant of the parent strain RN4220 (1, 8), in the presence of vancomycin Lab/Engineered 306551 Staphylococcus aureus subsp. aureus Z172 NC_022604.1,NC_022610.1,NC_022605.1 1 2 Hospital isolate from Taiwan Clinical/Human-associated 105558 Staphylococcus carnosus subsp. carnosus TM300 NC_012121 1 0 Fermented meat Food-associated 113981 Staphylococcus epidermidis ATCC 12228 NC_004461,NC_005008,NC_005007,NC_005006,NC_005005,NC_005004,NC_005003 1 6 man with bronchomycosis Clinical/Human-associated 130894 Staphylococcus epidermidis RP62A NC_002976,NC_006663 1 1 patient with intravascular catheter-associated sepsis isolated from a patient with intravascular catheter-associated sepsis Clinical/Human-associated 67511 Staphylococcus haemolyticus JCSC1435 NC_007168,NC_007170,NC_007171,NC_007169 1 3 Japanese inpatient at Juntendo Hospital, Tokyo, isolated from a Japanese inpatient at Juntendo Hospital, Tokyo, in 2000 Clinical/Human-associated 155172 Staphylococcus lugdunensis HKU09-01 NC_013893 1 0 patient suffering from skin and soft tissue infection isolated from a patient suffering from skin and soft tissue infection Clinical/Human-associated 214359 Staphylococcus lugdunensis N920143 NC_017353 1 0 Human breast abscess Clinical/Human-associated 308590 Staphylococcus pasteuri SP1 NC_022737.1 1 0 unknown 182428 Staphylococcus pseudintermedius ED99 NC_017568 1 0 Clinical/Human-associated isolate. Clinical/Human-associated 177932 Staphylococcus pseudintermedius HKU10-03 NC_014925 1 0 skin swab of a dog suffering from canine pyoderma. cultured from the skin swab of a dog suffering from canine pyoderma. Terrestrial-animal-associated 90642 Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 NC_007350,NC_007352,NC_007351 1 2 human urine specimen was from a human urine specimen Clinical/Human-associated 241197 Staphylococcus warneri SG1 NC_020164.1,NC_020268.1,NC_020266.1,NC_020269.1,NC_020165.1,NC_020264.1,NC_020274.1,NC_020265.1,NC_020267.1 1 8 Laboratory contaminant Lab/Engineered 45716 Starkeya novella DSM 506 NC_014217 1 0 soil soil 229363 Stenotrophomonas maltophilia D457 NC_017671 1 0 Clinical/Human-associated isolate Clinical/Human-associated 173823 Stenotrophomonas maltophilia JV3 NC_015947 1 0 Rhizopsphere Plant/agriculture-associated 45202 Stenotrophomonas maltophilia K279a NC_010943 1 0 blood infection isolated from blood infection and will be used for comparative genome analysis Clinical/Human-associated 40512 Stenotrophomonas maltophilia R551-3 NC_011071 1 0 the poplar Populus trichocarpa x deltoides cv isolated from the poplar Populus trichocarpa x deltoides cv Plant/agriculture-associated 183207 Strawberry lethal yellows phytoplasma (CPA) str. NZSb11 NC_021236 1 0 Plant/agriculture-associated 53754 Streptobacillus moniliformis DSM 12112 NC_013515,NC_013516 1 1 case of rat bite fever isolated from a case of rat bite fever and will provide information on the pathogenicity and virulence mechanisms of this organism Clinical/Human-associated 296025 Streptococcus agalactiae 09mas018883 NC_021485 1 0 Milk of a cow with clinical mastitis Terrestrial-animal-associated Streptococcus agalactiae 2-22 (serotype Ib) NC_021195 1 0 fish pathogen isolated from fish and other poikilotherms. Aquatic-life-associated 72745 Streptococcus agalactiae 2603V/R NC_004116 1 0 Clinical/Human-associated isolate Clinical/Human-associated 82541 Streptococcus agalactiae A909 NC_007432 1 0 septic human neonate Clinical/Human-associated 243097 Streptococcus agalactiae GD201008-001 NC_018646 1 0 tilapia isolate from cultured tilapia in China Aquatic-life-associated 293244 Streptococcus agalactiae ILRI005 NC_021486 1 0 One-Humped Camel Terrestrial-animal-associated 294070 Streptococcus agalactiae ILRI112 NC_021507 1 0 milk of camel from Kenya isolated from milk of camel from Kenya Terrestrial-animal-associated 3577 Streptococcus agalactiae NEM316 NC_004368 1 0 case of fatal septicemia isolated from a case of fatal septicemia Clinical/Human-associated Streptococcus agalactiae SA20-06 NC_019048 1 0 isolated from a meningoencephalitis outbreak in Nile tilapia (Oreochromis niloticus) from Brazil, Nile tilapia Aquatic-life-associated 164707 Streptococcus anginosus C1051 NC_022244.1 1 0 an invasive isolate Clinical/Human-associated 166616 Streptococcus anginosus C238 NC_022239.1 1 0 a respiratory isolate Clinical/Human-associated 165753 Streptococcus constellatus subsp. pharyngis C1050 NC_022238.1 1 0 an invasive isolate from a non-related individual Clinical/Human-associated 156888 Streptococcus constellatus subsp. pharyngis C232 NC_022236 1 0 respiratory strains isolated from one individual Clinical/Human-associated 166784 Streptococcus constellatus subsp. pharyngis C818 NC_022245 1 0 respiratory strains isolated from one individual Clinical/Human-associated 299855 Streptococcus dysgalactiae subsp. equisimilis 167 NC_022532 1 0 infected humans Clinical/Human-associated 152936 Streptococcus dysgalactiae subsp. equisimilis AC-2713 NC_019042 1 0 blood from a 78-year-old male patient with history of liver cirrhosis due to chronic hepatitis C Clinical/Human-associated 144480 Streptococcus dysgalactiae subsp. equisimilis ATCC 12394 NC_017567 1 0 Collected in 1939 from a blister of a child with epidermolysis bullosa, an inherited skin disorder that causes blistering in response to minor injury. Clinical/Human-associated 95162 Streptococcus dysgalactiae subsp. equisimilis GGS_124 NC_012891 1 0 isolated from human infections Clinical/Human-associated 262779 Streptococcus dysgalactiae subsp. equisimilis RE378 NC_018712 1 0 isolated from human infections Clinical/Human-associated 13040 Streptococcus equi subsp. equi 4047 NC_012471 1 0 horse with strangles from New Forest, UK Terrestrial-animal-associated 35012 Streptococcus equi subsp. zooepidemicus NC_012470 1 0 Nasal swab taken from a healthy Thoroughbred racehorse from Newmarket, UK Terrestrial-animal-associated 204605 Streptococcus equi subsp. zooepidemicus ATCC 35246 NC_017582 1 0 dead pig in Sichuan province, China Terrestrial-animal-associated 17662 Streptococcus equi subsp. zooepidemicus MGCS10565 NC_011134 1 0 throat of a patient with nephritis diagnosed during an epidemic in the state of Minas Gerais, Brazil Clinical/Human-associated 184003 Streptococcus gallolyticus subsp. gallolyticus ATCC 43143 NC_017576 1 0 Human blood Clinical/Human-associated 182109 Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069 NC_015215,NC_015219 1 1 human blood culture; infective endocarditis Clinical/Human-associated 150982 Streptococcus gallolyticus UCN34 NC_013798 1 0 patient responsible for endocarditis in a patient also suffering from colon cancer Clinical/Human-associated 124371 Streptococcus gordonii str. Challis substr. CH1 NC_009785 1 0 dental plaque Clinical/Human-associated 221872 Streptococcus infantarius subsp. infantarius CJ18 NC_016826,NC_016837 1 1 African dairy isolate local camel milk market in Mandera, Kenya Food-associated 297533 Streptococcus iniae SF1 NC_021314 1 0 Aquatic-life-associated 166724 Streptococcus intermedius B196 NC_022246 1 0 an invasive isolate obtained from a CF patient coinciding with a pulmonary exacerbation. Clinical/Human-associated 165427 Streptococcus intermedius C270 NC_022237 1 0 a respiratory isolate Clinical/Human-associated 27041 Streptococcus intermedius JTH08 NC_018073 1 0 unknown 228485 Streptococcus lutetiensis 033 NC_021900 1 0 a diarrheal child Clinical/Human-associated 222691 Streptococcus macedonicus ACA-DC 198 NC_016749,NC_016750 1 1 Isolated from naturally fermented Greek kasseri cheese. Food-associated 3699 Streptococcus mitis B6 NC_013853 1 0 hospital isolated from a hospital in Bochum, Germany Clinical/Human-associated 249475 Streptococcus mutans GS-5 NC_018089 1 0 isolated from human carious lesions Clinical/Human-associated Streptococcus mutans LJ23 (serotype k) NC_017768 1 0 Isolated from the oral cavity of a Japanese patient. Clinical/Human-associated 11111 Streptococcus mutans NN2025 NC_013928 1 0 isolated in Japan in 2002 Clinical/Human-associated 61772 Streptococcus mutans UA159 NC_004350 1 0 child with active dental caries isolated from a child with active dental caries in 1982 Clinical/Human-associated 281368 Streptococcus oligofermentans AS 1.3089 NC_021175 1 0 caries-free human, dental plaque Clinical/Human-associated 177080 Streptococcus oralis Uo5 NC_015291 1 0 human mouth Clinical/Human-associated Streptococcus parasanguinis ATCC 15912 NC_015678 1 0 Human throat Clinical/Human-associated 237648 Streptococcus parasanguinis FW213 NC_017905 1 0 human dental plaque Clinical/Human-associated 182031 Streptococcus parauberis KCTC 11537 NC_015558 1 0 isolated from the spleen of diseased olive flounder collected from an aquaculture farm in Jeju Island, South Korea, in 2006 Aquatic-life-associated 183593 Streptococcus pasteurianus ATCC 43144 NC_015600 1 0 Human blood Clinical/Human-associated 54539 Streptococcus pneumoniae 670-6B NC_014498 1 0 Spain isolated in 1988 from Spain and is a serotype 6B isolate Clinical/Human-associated 83895 Streptococcus pneumoniae 70585 NC_012468 1 0 Clinical/Human-associated 312907 Streptococcus pneumoniae A026 NC_022655 1 0 a Clinical/Human-associated multidrug-resistant isolate. Clinical/Human-associated 98725 Streptococcus pneumoniae AP200 NC_014494 1 0 the cerebrospinal fluid of a patient with meningitis isolate from the cerebrospinal fluid of a patient with meningitis in Italy in 2003 Clinical/Human-associated 132160 Streptococcus pneumoniae ATCC 700669 NC_011900 1 0 A multidrug resistant pneumococcal pandemic lineage Streptococcus pneumoniae Spain 23F ST81 Clinical/Human-associated 123335 Streptococcus pneumoniae CGSP14 NC_010582 1 0 Clinical/Human-associated 27904 Streptococcus pneumoniae D39 NC_008533 1 0 Clinical isolate in 1916, used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. derived from strain D39 Clinical/Human-associated 77426 Streptococcus pneumoniae G54 NC_011072 1 0 respiratory sample isolated in Genova Italy by G. Schito from a respiratory sample in 1991 Clinical/Human-associated 260105 Streptococcus pneumoniae gamPNI0373 NC_018630 1 0 normal human nasopharyngeal flora Clinical/Human-associated 34925 Streptococcus pneumoniae Hungary19A-6 NC_010380 1 0 Clinical/Human-associated 166045 Streptococcus pneumoniae INV104 NC_017591 1 0 Clinical/Human-associated 166962 Streptococcus pneumoniae INV200 NC_017593 1 0 Clinical/Human-associated 71544 Streptococcus pneumoniae JJA NC_012466 1 0 Brazil Clinical/Human-associated 166247 Streptococcus pneumoniae OXC141 NC_017592 1 0 Clinical/Human-associated 91701 Streptococcus pneumoniae P1031 NC_012467 1 0 ghana african Clinical/Human-associated isolate Clinical/Human-associated 107296 Streptococcus pneumoniae R6 NC_003098 1 0 USA S. pneumoniae R6 is a descendant of the type 2 capsule S (smooth or encapsulated) Clinical/Human-associated isolate used by Avery and coworkers to demonstrate the genetic function of DNA Clinical/Human-associated 166708 Streptococcus pneumoniae SPN034156 NC_021006 1 0 unknown 165971 Streptococcus pneumoniae SPN034183 NC_021028 1 0 unknown 168638 Streptococcus pneumoniae SPN994038 NC_021026 1 0 unknown 164986 Streptococcus pneumoniae SPN994039 NC_021005 1 0 Glasgow Reference Lab unknown Streptococcus pneumoniae SPNA45 NC_018594 1 0 unknown 239915 Streptococcus pneumoniae ST556 NC_017769 1 0 middle ear fluid sample Clinical/Human-associated 22502 Streptococcus pneumoniae Taiwan19F-14 NC_012469 1 0 cerebrospinal fluid, Taiwan Clinical/Human-associated 36006 Streptococcus pneumoniae TCH8431/19A NC_014251 1 0 respiratory tract Clinical/Human-associated 105772 Streptococcus pneumoniae TIGR4 NC_003028 1 0 the blood of a 30 year old male patient isolate from the blood of a 30 year old male patient in Kongsvinger, Norway Clinical/Human-associated 205216 Streptococcus pseudopneumoniae IS7493 NC_015875,NC_015876 1 1 sputum of a patient with human immunodeficiency virus (HIV) who had documented pneumonia Isolate IS7493 was obtained from the sputum of a patient with human immunodeficiency virus (HIV) who had documented pneumonia Clinical/Human-associated 262356 Streptococcus pyogenes A20 NC_018936.1 1 0 Necrotizing fasciitis patient isolated from a Necrotizing fasciitis patient in Tainan Provincial Hospital, ROC Clinical/Human-associated 85850 Streptococcus pyogenes Alab49 NC_017596 1 0 Recovered from an impetigo lesion in Alabama in 1986. impetigo lesion from human Clinical/Human-associated 311917 Streptococcus pyogenes HSC5 NC_021807.1 1 0 unknown 249099 Streptococcus pyogenes M1 476 NC_020540.1 1 0 streptococcal toxic shock syndrome case (STSS) during pregnancy isolated from a streptococcal toxic shock syndrome case (STSS) during pregnancy Clinical/Human-associated 79812 Streptococcus pyogenes M1 GAS NC_002737 1 0 patient with a wound infection isolated from a patient with a wound infection Clinical/Human-associated 120482 Streptococcus pyogenes MGAS10270 NC_008022 1 0 pharyngeal swab fron child Clinical/Human-associated 30273 Streptococcus pyogenes MGAS10394 NC_006086 1 0 child with pharyngitis This strain is a serotype M6 isolate cultured from a child with pharyngitis in private elementary school in Pennsilvania. Clinical/Human-associated 25933 Streptococcus pyogenes MGAS10750 NC_008024 1 0 human pharyngeal swab from patient with pharyngitis Clinical/Human-associated 163622 Streptococcus pyogenes MGAS15252 NC_017040 1 0 soft tissue infection Clinical/Human-associated 227283 Streptococcus pyogenes MGAS1882 NC_017053 1 0 Clinical/Human-associated 133020 Streptococcus pyogenes MGAS2096 NC_008023 1 0 patient with acute poststreptococcal glomerulonephritis Clinical/Human-associated 96585 Streptococcus pyogenes MGAS315 NC_004070 1 0 patient with streptococcal toxic shock syndrome Clinical/Human-associated 7871 Streptococcus pyogenes MGAS5005 NC_007297 1 0 invasive case isolated from an invasive case in Ontario Clinical/Human-associated 35950 Streptococcus pyogenes MGAS6180 NC_007296 1 0 invasive disease isolated from an invasive disease in Texas in 1998 and is an M28 serotype Clinical/Human-associated 4396 Streptococcus pyogenes MGAS8232 NC_003485 1 0 throat swab from patient with acute rheumatic fever Clinical/Human-associated 37061 Streptococcus pyogenes MGAS9429 NC_008021 1 0 pharyngeal swab from animal Terrestrial-animal-associated 129711 Streptococcus pyogenes NZ131 NC_011375 1 0 patient with acute glomerulonephritis isolated from a patient with acute glomerulonephritis Clinical/Human-associated 110589 Streptococcus pyogenes SSI-1 NC_004606 1 0 toxic-shock patient isolated from a toxic-shock patient in Japan and often associated with severe invasive infections, necrotizing fasciitis, and death Clinical/Human-associated 41547 Streptococcus pyogenes str. Manfredo NC_009332 1 0 patient isolated from a patient in the 1950's in Chicago Clinical/Human-associated 205187 Streptococcus salivarius 57.I NC_017594 1 0 oral cavity Clinical/Human-associated 117533 Streptococcus salivarius JIM8777 NC_017595 1 0 isolated from oral cavity of a healthy dentate infant Clinical/Human-associated 202804 Streptococcus salivarius JIM8780 NC_015760 1 0 Clinical/Human-associated 33173 Streptococcus sanguinis SK36 NC_009009 1 0 human dental plaque isolated from human dental plaque in 1980 and is virulent in a rat model Clinical/Human-associated 239066 Streptococcus sp. I-G2 NC_022584 1 0 ileal fluid Human ileal fluid Clinical/Human-associated 236783 Streptococcus sp. I-P16 NC_022582 1 0 ileal fluid Human ileal fluid Clinical/Human-associated 128929 Streptococcus suis 05ZYH33 NC_009442 1 0 Chinese virulent strain isolated from fatal cases of STSS in 2005 Clinical/Human-associated 72275 Streptococcus suis 98HAH33 NC_009443 1 0 isolated from fatal cases of streptococcal toxic shock syndrome in 1998 and 2005 Clinical/Human-associated 183084 Streptococcus suis A7 NC_017622 1 0 china unknown 1141 Streptococcus suis BM407 NC_012926,NC_012923 1 1 Clinical/Human-associated isolate Streptococcus suis BM407 is a human Clinical/Human-associated isolate Clinical/Human-associated 188457 Streptococcus suis D12 NC_017621 1 0 china unknown 188324 Streptococcus suis D9 NC_017620 1 0 china unknown 127079 Streptococcus suis GZ1 NC_017617 1 0 Isolated in 2005 from a patient in China who had septicemia. Clinical/Human-associated 181850 Streptococcus suis JS14 NC_017618 1 0 Isolated from articulation of a diseased pig in Jiangsu Province, China. Terrestrial-animal-associated 84581 Streptococcus suis P1/7 NC_012925 1 0 isolated from an ante-mortem blood culture from a pig dying with meningitis Terrestrial-animal-associated 247324 Streptococcus suis S735 NC_018526.1 1 0 Diseased swine, 1963, Netherlands Isolated from a case of pneumonia in a pig. Terrestrial-animal-associated 269954 Streptococcus suis SC070731 NC_020526.1 1 0 Terrestrial-animal-associated 134201 Streptococcus suis SC84 NC_012924 1 0 Isolated from a case of streptococcal toxic shock-like syndrome in Sichuan Province, China in 2005. Streptococcus suis SC84 is a human Clinical/Human-associated isolate Clinical/Human-associated 189252 Streptococcus suis SS12 NC_017619 1 0 unknown 186919 Streptococcus suis ST1 NC_017950 1 0 isolated from CSF from a human case of meningitis in Ho Chi Minh City, Vietnam in 2004 Clinical/Human-associated 186933 Streptococcus suis ST3 NC_015433 1 0 Isolated from a pig with pneumonia in Hubei province, China. Terrestrial-animal-associated 310778 Streptococcus suis T15 NC_022665.1 1 0 healthy swine, Holland Terrestrial-animal-associated 289493 Streptococcus suis TL13 NC_021213.1 1 0 Terrestrial-animal-associated 303275 Streptococcus suis YB51 NC_022516.1 1 0 Terrestrial-animal-associated 135799 Streptococcus thermophilus CNRZ1066 NC_006449 1 0 yogurt isolated from yogurt in France Food-associated 208393 Streptococcus thermophilus JIM 8232 NC_017581.1 1 0 Isolated from milk. Food-associated 129203 Streptococcus thermophilus LMD-9 NC_008532,NC_008500,NC_008501 1 2 Food-associated 97850 Streptococcus thermophilus LMG 18311 NC_006448 1 0 commercial yogurt isolated from commercial yogurt in 1974 in the United Kingdom and is easily manipulated genetically Food-associated 251338 Streptococcus thermophilus MN-ZLW-002 NC_017927 1 0 originally isolated from traditionally fermented Chinese dairy products. originally isolated from traditionally fermented Chinese dairy products. Food-associated 160185 Streptococcus thermophilus ND03 NC_017563 1 0 traditional dairy products of minority nationalities Isolated from naturally fermented yak milk in Qinghai, China. Food-associated 20775 Streptococcus uberis 0140J NC_012004 1 0 clinical bovine mastitis case Isolated from milk obtained from a clinical case of bovine mastitis in 1972 within the UK. Terrestrial-animal-associated Streptomyces albus J1074 NC_020990 1 0 treptomyces albus J1074 is a derivative of S. albus G, defective in both restriction and modification enzymes of the SalI system Lab/engineered 112782 Streptomyces avermitilis MA-4680 NC_003155,NC_004719 1 1 soil sample collected isolated and characterized in 1978 by R. Burg and colleagues from a soil sample collected in Shizuoka Prefecture, Japan soil 158249 Streptomyces bingchenggensis BCW-1 NC_016582 1 0 soil sample collected isolated from a soil sample collected in Harbin, China soil 216866 Streptomyces cattleya DSM 46488 NC_017586,NC_017585 1 1 Soil soil 187362 Streptomyces cattleya NRRL 8057 NC_016111,NC_016113 1 1 Soil soil 124346 Streptomyces coelicolor A3(2) NC_003888,NC_003903,NC_003904 1 2 Saprophytic bacteria producing most Natural environment antibiotics soil 257084 Streptomyces collinus Tu 365 NC_021985.1,NC_021986.1,NC_022001.1 1 2 Soil soil 258637 Streptomyces davawensis JCM 4913 NC_020504.1,NC_020545.1 1 1 obtained from the Japan Collection of Microorganisms (JCM) first isolated from a Philippine soil sample soil 287543 Streptomyces fulvissimus DSM 40593 NC_021177.1 1 0 unknown 32265 Streptomyces griseus subsp. griseus NBRC 13350 NC_010572 1 0 Soil bacterium producing an antituberculosis agent. soil 217687 Streptomyces hygroscopicus subsp. jinggangensis 5008 NC_017765.1,NC_016972.1,NC_017766.1 1 2 isolated from the Jinggang Mountain area of China in 1974 soil 242072 Streptomyces hygroscopicus subsp. jinggangensis TL01 NC_020895.1,NC_020293.1,NC_020894.1 1 2 soil 115143 Streptomyces pratensis ATCC 33331 NC_016114,NC_016110,NC_016115 1 2 Soil soil 290735 Streptomyces rapamycinicus NRRL 5491 NC_022785.1 1 0 a soil sample collected on Easter Island soil 144334 Streptomyces scabiei 87.22 NC_013929 1 0 Isolated in Wisconsin, United States. Plant/agriculture-associated 275382 Streptomyces sp. PAMC26508 NC_021055.1,NC_021056.1 1 1 algae-associated Insect-associated/other symbiont 183877 Streptomyces venezuelae ATCC 10712 NC_018750 1 0 a wild-type strain unknown 112010 Streptosporangium roseum DSM 43021 NC_013595,NC_013596 1 1 Isolated from vegetable garden soil. soil 142080 Sulfobacillus acidophilus DSM 10332 NC_016884,NC_016888 1 1 unknown 211607 Sulfobacillus acidophilus TPY NC_015757.1 1 0 isolated from a hydrothermal vent in the Pacific Ocean Extreme-environment 150841 Sulfuricurvum kujiense DSM 16994 NC_014762,NC_014763,NC_014754,NC_014755,NC_014756 1 4 solated from an underground crude-oil storage cavity Extreme-environment 123226 Sulfurihydrogenibium azorense Az-Fu1 NC_012438 1 0 terrestrial hot spring isolated from a terrestrial hot spring in the Azores, where it was living at temperatures between 65oC and 70oC Extreme-environment 94719 Sulfurihydrogenibium sp. YO3AOP1 NC_010730 1 0 Isolated from near-neutral-pH terrestrial hot springs in Obsidian Pool in Yellowstone National Park, USA. Extreme-environment 92361 Sulfurimonas autotrophica DSM 16294 NC_014506 1 0 Isolated from the surface of a deep-sea hydrothermal sediment on the Hatoma Knoll in the Mid-Okinawa Trough hydrothermal field. Extreme-environment 68967 Sulfurimonas denitrificans DSM 1251 NC_007575 1 0 Isolated from coastal marine sediments. isolated isolated from estuarine mud in the Netherlands Aquatic-environment 163455 Sulfurospirillum barnesii SES-3 NC_018002.1 1 0 "isolated from a selenate- contaminated freshwater marsh in western Nevada (Oremland et al., 1989, 1994)" Polluted/impacted environment 109514 Sulfurospirillum deleyianum DSM 6946 NC_013512 1 0 Isolated from anoxic mud of a forest pond near Heinigen, Braunschweig area, Germany. Aquatic-environment 49917 Sulfurovum sp. NBC37-1 NC_009663 1 0 deep-sea hydrothermal vent isolated from a deep-sea hydrothermal vent in the Iheya North field in the Mid-Okinawa Trough as part of a larger diversity study Extreme-environment 116959 Symbiobacterium thermophilum IAM 14863 NC_006177 1 0 isolated from compost Plant/agriculture-associated 117686 Synechococcus elongatus PCC 6301 NC_006576 1 0 freshwater Aquatic-environment 51371 Synechococcus elongatus PCC 7942 NC_007595,NC_007604 1 1 freshwater Aquatic-environment 88089 Synechococcus sp. CC9311 NC_008319 1 0 the oligotrophic edge of the California Current isolated in 1993 from the oligotrophic edge of the California Current Aquatic-environment 8993 Synechococcus sp. CC9605 NC_007516 1 0 photosynthesis related Top 2mm of microbial mat samples from Octopus Spring Yellowstone Extreme-environment 76179 Synechococcus sp. CC9902 NC_007513 1 0 seawater This strain was isolated from coastal seawater Aquatic-environment 29577 Synechococcus sp. JA-2-3B'a(2-13) NC_007776 1 0 Samples were obtained from the microbial mat in Octopus Spring, Yellowstone National Park Extreme-environment 90045 Synechococcus sp. JA-3-3Ab NC_007775 1 0 Samples were obtained from the microbial mat in Octopus Spring, Yellowstone National Park Extreme-environment 54615 Synechococcus sp. PCC 6312 NC_019680.1,NC_019681.1 1 1 fresh water Aquatic-environment 37135 Synechococcus sp. PCC 7002 NC_010475,NC_010476,NC_010477,NC_010478,NC_010479,NC_010480,NC_010474 1 6 onshore, marine mud flat sample derived from fish pens on Maguyes Island, La Parguera, Puerto Rico isolated in 1961 by Chase Van Baalen from an onshore, marine mud flat sample derived from fish pens on Maguyes Island, La Parguera, Puerto Rico Aquatic-environment 231034 Synechococcus sp. PCC 7502 NC_019702.1,NC_019692.1,NC_019691.1 1 2 sphagnum bog Aquatic-environment 108374 Synechococcus sp. RCC307 NC_009482 1 0 seawater This strain was isolated from seawater taken at a depth of 15 meters from the Mediterranean Sea Aquatic-environment 43824 Synechococcus sp. WH 7803 NC_009481 1 0 Sargasso Sea isolated from Sargasso Sea and will be used for comparative genomics Aquatic-environment 27240 Synechococcus sp. WH 8102 NC_005070 1 0 the tropical Atlantic ocean isolated from the tropical Atlantic ocean in 1981 Aquatic-environment 132158 Synechocystis sp. PCC 6803 NC_000911,NC_005231,NC_005232,NC_005229,NC_005230 1 4 freshwater lake isolated from a freshwater lake in 1968 and is easily transformed by exogenous DNA Aquatic-environment 223545 Synechocystis sp. PCC 6803 substr. PCC-N NC_017052.1 1 0 Freshwater lake in 1968 frozen stocks in the laboratory of Dr Masahiko Ikeuchi at The University of Tokyo, Japan. Aquatic-environment 220749 Synechocystis sp. PCC 6803 substr. PCC-P NC_017039 1 0 Freshwater lake in 1968 frozen stocks in the laboratory of Dr Masahiko Ikeuchi at The University of Tokyo, Japan. Aquatic-environment 78438 Syntrophobacter fumaroxidans MPOB NC_008554 1 0 granular sludge from an anaerobic sludge bed reactor treating sugar-beet processing wastewater isolated from granular sludge from an anaerobic sludge bed reactor treating sugar-beet processing wastewater Polluted/impacted environment 105927 Syntrophobotulus glycolicus DSM 8271 NC_015172 1 0 isolated from syntrophic coculture FlGlyM (DSM 6945), which was isolated from anoxic sewage sludge Polluted/impacted environment 51738 Syntrophomonas wolfei subsp. wolfei str. Goettingen NC_008346 1 0 anaerobic digestor sludge isolated from anaerobic digestor sludge and is the type strain of this species Polluted/impacted environment 21176 Syntrophothermus lipocalidus DSM 12680 NC_014220 1 0 granular sludge isolated from granular sludge in a thermophilic upflow anaerobic sludge blanket (UASB) reactor Polluted/impacted environment 70500 Syntrophus aciditrophicus SB NC_007759 1 0 sludge from a sewage treatment plant isolated from sludge from a sewage treatment plant in Norman, Oklahoma Polluted/impacted environment 42681 Tannerella forsythia ATCC 43037 NC_016610 1 0 human periodontal pocket isolated from a human periodontal pocket in Massachusetts and is the type strain for this organism Clinical/Human-associated 200180 Taylorella asinigenitalis MCE3 NC_016043 1 0 donkey jack genital tract of a 6-year-old donkey jack Terrestrial-animal-associated Taylorella equigenitalis 14/56 NC_021036 1 0 Isolated from a stallion during routine pre-export checks in Dubai in 2009. Terrestrial-animal-associated Taylorella equigenitalis ATCC 35865 NC_018108 1 0 horse Terrestrial-animal-associated 178523 Taylorella equigenitalis MCE9 NC_014914 1 0 the urethral fossa of a 4-year-old stallion from a stud farm isolated in 2005 from the urethral fossa of a 4-year-old stallion from a stud farm in the Haute-Savoie, France Terrestrial-animal-associated 247443 Tepidanaerobacter acetatoxydans Re1 NC_019954.1 1 0 mesophilic methanogenic systems isolated from mesophilic methanogenic systems Polluted/impacted environment 18581 Tepidanaerobacter sp. Re1 NC_015519 1 0 isolated from an ammonium-rich, mesophilic, methanogenic a continuously stirred laboratory-scale reactor designated Recirc that operated at 37 ?C and was fed with alfalfa silage Polluted/impacted environment 118718 Teredinibacter turnerae T7901 NC_012997 1 0 the gills of the wood-boring mollusc (Bivalvia:Teredinidae) and may potentially be useful isolated from the gills of the wood-boring mollusc (Bivalvia:Teredinidae) and may potentially be useful in biofuel production Aquatic-life-associated 185629 Terriglobus roseus DSM 18391 NC_018014.1 1 0 soil from a never-tilled, successional plant community at the Michigan State University Kellogg Biological Station Long-Term Ecological Research site soil 54836 Terriglobus saanensis SP1PR4 NC_014963 1 0 the Saana fell, Arctic-alpine tundra of Lappland isolated from the Saana fell, Arctic-alpine tundra of Lappland, soil soil 281250 Thalassolituus oleivorans MIL-1 NC_020888.1 1 0 sea water sediment collected from a depth of about 5 meters Aquatic-environment 83776 Thauera sp. MZ1T NC_011662,NC_011667 1 1 Wastewater treatment plant Polluted/impacted environment 225633 Thermacetogenium phaeum DSM 12270 NC_018870.1 1 0 Thermophilic (60c) anaerobic methanogenic reactor from kraft-pulp production plant in Japan Extreme-environment 50867 Thermaerobacter marianensis DSM 12885 NC_014831 1 0 mud from the Challenger Deep in the Mariana Trench at a depth of 10897m Aquatic-environment 125881 Thermanaerovibrio acidaminovorans DSM 6589 NC_013522 1 0 Upflow anaerobic sludge bed reactor of a sugar refinery, Breda, the Netherlands Production-site-facility 141296 Thermincola potens JR NC_014152 1 0 sludge reactor East Bay, MUD, Oakland, CA Production-site-facility 57020 Thermoanaerobacter brockii subsp. finnii Ako-1 NC_014964 1 0 lake sediment isolated from lake sediment in Africa Aquatic-environment 22270 Thermoanaerobacter italicus Ab9 NC_013921 1 0 Mud, thermal spa; Italy, Abano Terme Extreme-environment 18 Thermoanaerobacter mathranii subsp. mathranii str. A3 NC_014209 1 0 hot spring isolated from a hot spring in Iceland Extreme-environment 6203 Thermoanaerobacter pseudethanolicus ATCC 33223 NC_010321 1 0 Thermal springs in Yellowstone National Park Extreme-environment 170299 Thermoanaerobacter siderophilus SR4 NZ_CM001486.1 1 0 Hydrothermal vent Extreme-environment 86957 Thermoanaerobacter sp. X514 NC_010320 1 0 deep subsurface sample (2000 m below the surface) taken from a core hole at the Piceance Basin, Colorado, USA isolated by anaerobic enrichment culture from a deep subsurface sample (2000 m below the surface) taken from a core hole at the Piceance Basin, Colorado, USA Aquatic-environment 82880 Thermoanaerobacter tengcongensis MB4 NC_003869 1 0 hot spring isolated from a hot spring in Tengcong, China, and is the type strain for the species Extreme-environment 207413 Thermoanaerobacterium saccharolyticum JW/SL-YS485 NC_017992.1,NC_017998.1 1 1 Hot spring sediment. derived sugars, to produce ethanol Extreme-environment 89703 Thermoanaerobacterium thermosaccharolyticum DSM 571 NC_014410 1 0 Extreme-environment 177294 Thermoanaerobacterium thermosaccharolyticum M0795 NC_019970.1,NC_019956.1 1 1 Extreme-environment 68767 Thermobaculum terrenum ATCC BAA-798 NC_013525,NC_013526 2 0 thermal soil isolated from thermal soil in Yellowstone National Park and will be used for comparative analysis with other thermophilic bacterium Extreme-environment 33945 Thermobifida fusca YX NC_007333 1 0 compost pile in the 1970's Plant/agriculture-associated 80272 Thermobispora bispora DSM 43833 NC_014165 1 0 decaying manure isolated from decaying manure Plant/agriculture-associated 52854 Thermocrinis albus DSM 14484 NC_013894 1 0 Grayish filaments collected from a hot streamlet in Hveragerthi, Iceland Extreme-environment 141235 Thermodesulfatator indicus DSM 15286 NC_015681 1 0 Deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge Indian Ocean Extreme-environment 195719 Thermodesulfobacterium geofontis OPF15 NC_015682 1 0 environmental clone sequence obtained from a hot spring at Yellowstone National Park Extreme-environment 156843 Thermodesulfobium narugense DSM 14796 NC_015499 1 0 Narugo hot spring; Japan Extreme-environment 104483 Thermodesulfovibrio yellowstonii DSM 11347 NC_011296 1 0 Thermal vent in Yellowstone Lake in Wyoming Extreme-environment 91376 Thermomicrobium roseum DSM 5159 NC_011959,NC_011961 1 1 Yellowstone National Park isolated from Yellowstone National Park and will be used for comparative analysis with other thermophilic bacteria Extreme-environment 33965 Thermomonospora curvata DSM 43183 NC_013510 1 0 Municipal refuse compost samples isolated from straw and is the type strain Polluted/impacted environment 34679 Thermosediminibacter oceani DSM 16646 NC_014377 1 0 Deep sea sediments (252 m below sea level) of Peru Margin collected during Leg 201 of the Ocean Drilling Program Aquatic-environment 129358 Thermosipho africanus TCF52B NC_011653 1 0 the Troll oil formation isolated from the Troll oil formation in the North Sea and will be used for comparative analysis Extreme-environment 19269 Thermosipho melanesiensis BI429 NC_009616 1 0 the gills of Bathymodiolus brevior, a deep-seamussel isolated from the gills of Bathymodiolus brevior, a deep-seamussel Aquatic-life-associated 119873 Thermosynechococcus elongatus BP-1 NC_004113 1 0 Beppu hot spring isolated from Beppu hot spring in Japan Extreme-environment 311957 Thermosynechococcus sp. NK55 NC_023033.1 1 0 Nakabusa hot spring isolated from a green microbial mat at Nakabusa hot spring, Japan Extreme-environment 253338 Thermotoga elfii NBRC 107921 NC_022792.1 1 0 an African oil-producing well Extreme-environment 255279 Thermotoga hypogea NBRC 106472 NC_022795.1 1 0 Oil well in Africa Extreme-environment 125395 Thermotoga lettingae TMO NC_009828 1 0 methanol-degrading, sulfate-reducing bioreactor isolated from a methanol-degrading, sulfate-reducing bioreactor Polluted/impacted environment 51294 Thermotoga maritima MSB8 NC_000853 1 0 geothermal marine area near Vulcano, Italy isolated from a geothermal marine area near Vulcano, Italy Extreme-environment 72244 Thermotoga naphthophila RKU-10 NC_013642 1 0 Production fluid of the Kubiki oil reservoir in Niigata Japan Extreme-environment 118396 Thermotoga neapolitana DSM 4359 NC_011978 1 0 Black smoker in the bay near Naples Italy in 1986 Extreme-environment 65348 Thermotoga petrophila RKU-1 NC_009486 1 0 the production waters of the Kubiki oil reservoir isolated from the production waters of the Kubiki oil reservoir in Niigata, Japan Extreme-environment 108950 Thermotoga sp. RQ2 NC_010483 1 0 the geothermally heated seafloor isolated from the geothermally heated seafloor in the Azores Extreme-environment 149160 Thermotoga thermarum DSM 5069 NC_015707 1 0 Continental solfataric spring; Africa, Djibouti, Lac Abbe Extreme-environment 13058 Thermovibrio ammonificans HB-1 NC_014917,NC_014926 1 1 Walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9 degrees 50'N Extreme-environment 74131 Thermovirga lienii DSM 17291 NC_016148,NC_016149 1 1 Isolated from oil/water mixture collected at the upper-riser of a Norwegian oil reservoir. Production water from an oil well, Norway Extreme-environment 182939 Thermus oshimai JL-2 NC_019386.1,NC_019388.1,NC_019387.1 1 2 Sandy's Spring West (SSW), a >73˚C hot spring located in the U.S. Great Basin, Nevada Extreme-environment 147128 Thermus scotoductus SA-01 NC_014974,NC_014975 1 1 fissure water isolated from fissure water in a South African gold mine Extreme-environment 221235 Thermus sp. CCB_US3_UF1 NC_017278,NC_016634 1 1 Isolated from a hot spring in Ulu Slim, Perak, Malaysia, at 92.4 deg C, pH 7. Ulu Slim hot spring, Perak, Malaysia Extreme-environment 54392 Thermus thermophilus HB27 NC_005835,NC_005838 1 1 natural thermal environment isolated from a natural thermal environment in Japan Extreme-environment 93045 Thermus thermophilus HB8 NC_006461,NC_006463,NC_006462 1 2 hot spring isolated from a hot spring in Japan Extreme-environment 192969 Thermus thermophilus JL-18 NC_017587.1,NC_017588.1,NC_017590.1 1 2 Extreme-environment 168134 Thermus thermophilus SG0.5JP17-16 NC_017272,NC_017273 1 1 Extreme-environment 154341 Thioalkalimicrobium cyclicum ALM1 NC_015581 1 0 hypersaline alkaline Mono Lake Extreme-environment 264030 Thioalkalivibrio nitratireducens DSM 14787 NC_019902.1 1 0 soda lake Fazdah Extreme-environment 13812 Thioalkalivibrio sp. K90mix NC_013889,NC_013930 1 1 highly alkaline soda lake sediment isolated from highly alkaline soda lake sediment Extreme-environment 19295 Thioalkalivibrio sulfidophilus HL-EbGr7 NC_011901 1 0 sulfide-oxidizing bioreactor isolated from a sulfide-oxidizing bioreactor and will be used for comparative analysis Polluted/impacted environment 82923 Thiobacillus denitrificans ATCC 25259 NC_007404 1 0 soil from Texas, USA isolated from soil from Texas, USA soil 160332 Thioflavicoccus mobilis 8321 NC_019940.1,NC_019941.1 1 1 flat, laminated microbial mat in a salt marsh Extreme-environment 83387 Thiomicrospira crunogena XCL-2 NC_007520 1 0 deep-sea hydrothermal vent isolated from a deep-sea hydrothermal vent Extreme-environment Thiomonas arsenitoxydans NC_014145,NC_014144 1 1 Polluted/impacted environment 85915 Thiomonas intermedia K12 NC_014153,NC_014154,NC_014155 1 2 sewage pipe in Hamburg Germany Polluted/impacted environment 230605 Tistrella mobilis KA081020-065 NC_017956.1,NC_017959.1,NC_017958.1,NC_017966.1,NC_017957.1 1 4 from the Red Sea Aquatic-environment 42623 Tolumonas auensis DSM 9187 NC_012691 1 0 the sediment of a freshwater lake isolated from the sediment of a freshwater lake in Switzerland Aquatic-environment 94830 Treponema azotonutricium ZAS-9 NC_015577 1 0 hindgut of the Pacific dampwood termite Zootermopsis angusticollis Insect-associated/other symbiont 169731 Treponema brennaborense DSM 12168 NC_015500 1 0 Ulcerative lesion of a bovine foot infected with digital dermatitis Terrestrial-animal-associated 151796 Treponema caldaria DSM 7334 NC_015732 1 0 human periodontal pocket Clinical/Human-associated 445 Treponema denticola ATCC 35405 NC_002967 1 0 human periodontal pocket isolated from a human periodontal pocket and is the type strain of this organism Clinical/Human-associated 240291 Treponema pallidum str. Fribourg-Blanc NC_021179.1 1 0 isolated in 1966 from baboons (Papio cynocephalus) in West Africa Terrestrial-animal-associated 32381 Treponema pallidum subsp. pallidum DAL-1 NC_016844.1 1 0 Clinical/Human-associated 10923 Treponema pallidum subsp. pallidum SS14 NC_010741 1 0 patient with secondary syphilis isolated in 1977 from a patient with secondary syphilis Clinical/Human-associated 139508 Treponema pallidum subsp. pallidum str. Chicago NC_017268 1 0 isolated in 1951 Clinical/Human-associated 155572 Treponema pallidum subsp. pallidum str. Mexico A NC_018722.1 1 0 isolated in 1953 from male, with primary syphilis, living in Mexico Clinical/Human-associated 57110 Treponema pallidum subsp. pallidum str. Nichols NC_000919 1 0 neurosyphilitic patient; isolated in 1912 from the cerebrospinal fluid (CSF) of a patient with secondary syphilis isolated in 1912 from a neurosyphilitic patient and is virulent Clinical/Human-associated 82524 Treponema pallidum subsp. pertenue str. CDC2 NC_016848.1 1 0 This strain was isolated in Akorabo, Ghana in 1980 Clinical/Human-associated 1549 Treponema pallidum subsp. pertenue str. Gauthier NC_016843.1 1 0 This strain was isolated in Brazzaville, the Republic of Congo in 1960 Clinical/Human-associated 69077 Treponema pallidum subsp. pertenue str. SamoaD NC_016842.1 1 0 isolated in Western Samoa in 1953 and will be used for comparative analysis Clinical/Human-associated 15602 Treponema paraluiscuniculi Cuniculi A NC_015714 1 0 isolated from an infected rabbit. case of syphilis in a rabbit Terrestrial-animal-associated 265529 Treponema pedis str. T A4 NC_022097.1 1 0 isolated from a porcine necrotic ear lesion Terrestrial-animal-associated 14895 Treponema primitia ZAS-2 NC_015578 1 0 hindgut of the Pacific dampwood termite Zootermopsis angusticollis Insect-associated/other symbiont 166698 Treponema succinifaciens DSM 2489 NC_015385,NC_015386 1 1 colon of swine Terrestrial-animal-associated 99848 Trichodesmium erythraeum IMS101 NC_008312 1 0 the North Carolina coast isolated from the North Carolina coast in 1992 and grows in straight filaments Aquatic-environment 72342 Tropheryma whipplei str. Twist NC_004572 1 0 unknown 42739 Tropheryma whipplei TW08/27 NC_004551 1 0 the cerebrospinal fluid a woman who had suffered severe weight loss isolated from the cerebrospinal fluid a woman who had suffered severe weight loss in Germany Clinical/Human-associated 72214 Truepera radiovictrix DSM 17093 NC_014221 1 0 Water sample from a hot spring runoffs on the Island of Sao Miguel in the Azores, Portugal Extreme-environment 718 Tsukamurella paurometabola DSM 20162 NC_014158,NC_014159 1 1 ovaries of Cimex lectularius L (bedbug) Insect-associated/other symbiont 168040 Turneriella parva DSM 21527 NC_018020.1,NC_018021.1 1 1 contaminated bovine albumin liquid culture medium in Saskatchewan, Canada, in 1981 Lab/Engineered 275036 uncultured Sulfuricurvum sp. RIFRC-1 NC_020505,NC_020503 1 1 subsurface sediment from a freshwater well derived from soil and from bottle cultures innoculated with soil form the Old Rifle Uranium Mill Tailing site Extreme-environment 52152 uncultured Termite group 1 bacterium phylotype Rs-D17 NS_000191,NC_020420,NC_020421,NC_020422 1 3 The wood-feeding termite Reticulitermes speratus (Isoptera; Rhinotermitidae) was collected in Saitama, Japan. The entire gut was removed from a worker termite, and a single cell of the cellulolytic protist Trichonympha agilis (Parabasalia; Trichonymphida) in the gut was physically isolated by using a micromanipulator. Insect-associated/other symbiont 123156 Ureaplasma parvum serovar 3 str. ATCC 27815 NC_010503 1 0 human infected with nongonococcal urethritis Clinical/Human-associated 45146 Ureaplasma parvum serovar 3 str. ATCC 700970 NC_002162 1 0 lung tissue of a newborn infant, plancenta of patient obtained by E. Freundt at the Institue of Medical Microbiology, University of Aarhus, Aarhus, Denmark Clinical/Human-associated 98799 Ureaplasma urealyticum serovar 10 str. ATCC 33699 NC_011374 1 0 from the urethras of men with non-gonococcal urethritis in 1954 Clinical/Human-associated 264937 Variovorax paradoxus B4 NC_022247.1,NC_022234.1 2 0 polluted soil near a production plant of chemical industry due to its ability to utilize organic sulfur compounds isolated from polluted soil near a production plant of chemical industry due to its ability to utilize organic sulfur compounds Polluted/impacted environment 156291 Variovorax paradoxus EPS NC_014931 1 0 the rhizosphere community of the sunflower (Helianthus annuus) on the campus of California State University Plant/agriculture-associated 36677 Variovorax paradoxus S110 NC_012791,NC_012792 2 0 the interior of a potato plant grown in a farm of upstate New York Plant/agriculture-associated 80537 Veillonella parvula DSM 2008 NC_013520 1 0 isolated from the human intestinal tract Clinical/Human-associated 316718 Veillonella parvula HSIVP1 NC_013520 1 0 ileostomy effluent evening sample obtained from a 79 year-old male ileostomist plated on Veillonella selective agar Clinical/Human-associated 120356 Verminephrobacter eiseniae EF01-2 NC_008786,NC_008771 1 1 Kidney of the earthworm Eisenia foetida Insect-associated/other symbiont 92278 Verrucosispora maris AB-18-032 NC_015409,NC_015434 1 1 deep marine sediment sample collected from the East Sea (Sea of Japan) Aquatic-environment Vibrio alginolyticus NBRC 15630 = ATCC 17749 NC_022349,NC_022359 2 0 Spoiled horse mackerel which caused food poisoning, Japan food-associated 170577 Vibrio anguillarum 775 NC_015633,NC_015637 2 0 Oncorhynchus kisutch (Coho salmon) Aquatic-life-associated Vibrio campbellii ATCC BAA-1116 (Vibrio harveyi ATCC BAA-1116) NC_022269,NC_022270,NC_022271 2 1 ocean isolate Aquatic-environment Vibrio campbellii ATCC BAA-1116 (Vibrio harveyi ATCC BAA-1116) NC_009783,NC_009784,NC_009777 2 1 ocean isolate Aquatic-environment 238670 Vibrio cholerae IEC224 NC_016945.1,NC_016944.1 2 0 stool sample isolated in November of 1994 at the city of Bel??m/Pa from a stool sample Clinical/Human-associated 179000 Vibrio cholerae LMA3894-4 NC_017270,NC_017269 2 0 isolated in 2007 from the Tucunduba Igarapé (small first order Amazonian tributary) water of Tucunduba creek Aquatic-environment 108967 Vibrio cholerae M66-2 NC_012578,NC_012580 2 0 outbreak isolated from the 1937 cholera outbreak in the Makassar area of Indonesia Clinical/Human-associated 20143 Vibrio cholerae MJ-1236 NC_012668,NC_012667 2 0 from Matlab, Bangladesh, 1994 Clinical/Human-associated Vibrio cholerae O1 2010EL-1786 NC_016445,NC_016446 2 0 Haiti 2010 outbreak isolate. Clinical/Human-associated 83274 Vibrio cholerae O1 biovar El Tor str. N16961 NC_002505,NC_002506 2 0 the classical biotype due to hemolysin production stool from cholera patient in Epidemic outbreak in Bangladesh in 1971 Clinical/Human-associated 35538 Vibrio cholerae O395 NC_009456,NC_009457 2 0 6th pandemic strain, O395, was isolated in 1965 Clinical/Human-associated 203754 Vibrio cholerae O395 NC_009456,NC_009457 2 0 6th pandemic strain 6th pandemic strain, O395, was isolated in 1965 Clinical/Human-associated Vibrio cholerae O395 NC_012582,NC_012583 2 0 Strain of the 6th pandemic in South Asia, isolated in 1965. Clinical/Human-associated 127983 Vibrio fischeri ES114 NC_006840,NC_006841,NC_006842 2 1 the light organs of the squid Euprymna scolopes isolated from the light organs of the squid Euprymna scolopes Aquatic-life-associated 37164 Vibrio fischeri MJ11 NC_011186,NC_011184,NC_011185 2 1 fish light organ isolated from a fish light organ in Japan Aquatic-life-associated 169925 Vibrio furnissii NCTC 11218 NC_016602,NC_016628 2 0 Estaurine water Aquatic-environment 89376 Vibrio nigripulchritudo SnF1 NC_022543.1,NC_022528.1 2 0 from diseased shrimp Aquatic-life-associated 250154 Vibrio parahaemolyticus BB22OP NC_019971.1,NC_019955.1 2 0 environmental isolate from bangladesh 1980 marine isolate Aquatic-environment Vibrio parahaemolyticus O1:K33 CDC_K4557 NC_021848,NC_021822 2 0 unknown Vibrio parahaemolyticus O1:Kuk FDA_R31 NC_021847,NC_021821 2 0 unknown 50997 Vibrio parahaemolyticus RIMD 2210633 NC_004603,NC_004605 2 0 Clinical/Human-associated strain isolated in 1996 in Osaka Japan isolated in 1996 in Osaka, Japan Clinical/Human-associated 220376 Vibrio sp. EJY3 NC_016613,NC_016614 2 0 The coast of the West Sea at Incheon in Korea. Aquatic-environment 203755 Vibrio sp. Ex25 NC_013456,NC_013457 2 0 samples taken from a deep-sea hydrothermal vent community along the East Pacific Rise isolated from samples taken from a deep-sea hydrothermal vent community along the East Pacific Rise Extreme-environment 48387 Vibrio splendidus LGP32 NC_011753,NC_011744 2 0 Hollow oyster, Cassostrea gigas Aquatic-life-associated 94426 Vibrio vulnificus CMCP6 NC_004459,NC_004460 2 0 Clinical/Human-associated isolate from humans Clinical/Human-associated 176069 Vibrio vulnificus MO6-24/O NC_014965,NC_014966 2 0 patient with septicemia Clinical/Human-associated 40472 Vibrio vulnificus YJ016 NC_005139,NC_005140,NC_005128 2 1 Taiwan Hospital isolate from Taiwan Clinical/Human-associated 156037 Waddlia chondrophila WSU 86-1044 NC_014225,NC_014226 1 1 Pooled liver/lung homogenate from the aborted fetus of a 19-month-old primigravid Holstein cow during month 3 of gestation Terrestrial-animal-associated 165365 Weeksella virosa DSM 16922 NC_015144 1 0 Human urine; USA, North Carolina Clinical/Human-associated 209535 Weissella koreensis KACC 15510 NC_015756,NC_015759 1 1 Chinese cabbage kimchi Food-associated 15804 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis NC_004344,NC_003425 1 1 Insect-associated/other symbiont 43724 Wigglesworthia glossinidia endosymbiont of Glossina morsitans morsitans (Yale colony) NC_016893 1 0 tsetse fly Insect-associated/other symbiont 95846 Wolbachia endosymbiont of Culex quinquefasciatus Pel NC_010981 1 0 the preblastoderm embryos of the Pelstrain of Culex quinquefasciatus mosquitoes isolated from the preblastoderm embryos of the Pelstrain of Culex quinquefasciatus mosquitoes and will be used for comparative analysis with Wolbachia from other organisms Insect-associated/other symbiont 21207 Wolbachia endosymbiont of Drosophila melanogaster NC_002978 1 0 Insect-associated/other symbiont 297835 Wolbachia endosymbiont of Drosophila simulans wHa NC_021089 1 0 Insect-associated/other symbiont 297587 Wolbachia endosymbiont of Drosophila simulans wNo NC_021084 1 0 Insect-associated/other symbiont 119623 Wolbachia endosymbiont of Onchocerca ochengi str. Adamawa_Cameroon NC_018267 1 0 parasite cattle filarial Insect-associated/other symbiont 7741 Wolbachia endosymbiont strain TRS of Brugia malayi NC_006833 1 0 Insect-associated/other symbiont 98304 Wolbachia sp. wRi NC_012416 1 0 isolated from naturally infected and transinfected symbiotic associations of D. simulans Insect-associated/other symbiont 63014 Wolinella succinogenes DSM 1740 NC_005090 1 0 the rumen of a cow isolated from the rumen of a cow and is considered nonpathogenic in both its host and in humans Terrestrial-animal-associated 29526 Xanthobacter autotrophicus Py2 NC_009720,NC_009717 1 1 freshwater (ditch water) isolated with propene as a sole carbon and energy source Aquatic-environment 89132 Xanthomonas albilineans GPE PC73 NC_013722 1 0 isolated in Guadeloupe and is closely related to strains isolated in Asia, Africa, and North America Plant/agriculture-associated 33670 Xanthomonas axonopodis pv. citri str. 306 NC_003919,NC_003921,NC_003922 1 2 sugarcane, Saccharum officinarum Plant/agriculture-associated 186298 Xanthomonas axonopodis pv. citrumelo F1 NC_016010 1 0 Plant/agriculture-associated 279613 Xanthomonas axonopodis Xac29-1 NC_020800,NC_020797,NC_020798,NC_020801 1 3 Plant/agriculture-associated 24967 Xanthomonas campestris pv. campestris str. 8004 NC_007086 1 0 inflected cauliflower isolated from an inflected cauliflower in Sussex, United Kingdom, in 1958 Plant/agriculture-associated 115730 Xanthomonas campestris pv. campestris str. ATCC 33913 NC_003902 1 0 cabbage isolated from cabbage Plant/agriculture-associated 108527 Xanthomonas campestris pv. campestris str. B100 NC_010688 1 0 isolated in a screening that aimed at identifying a strain suitable for xanthan production Plant/agriculture-associated 194565 Xanthomonas campestris pv. raphani 756C NC_017271 1 0 isolated from cruciferous plants Plant/agriculture-associated 71633 Xanthomonas campestris pv. vesicatoria str. 85-10 NC_007508,NC_007504,NC_007505,NC_007506,NC_007507 1 4 Plant/agriculture-associated 235228 Xanthomonas citri subsp. citri Aw12879 NC_020815,NC_020817,NC_020816 1 2 Citrus grove in Wellington (Florida) from USA. Plant/agriculture-associated 78442 Xanthomonas fuscans subsp. fuscans str. 4834-R NC_022541,NC_022539,NC_022540,NC_022542 1 3 isolated from a seed-borne epidemic in France in 1998 bean leaves Plant/agriculture-associated 111333 Xanthomonas oryzae pv. oryzae KACC10331 NC_006834 1 0 Plant/agriculture-associated 49434 Xanthomonas oryzae pv. oryzae MAFF 311018 NC_007705 1 0 Plant/agriculture-associated 73153 Xanthomonas oryzae pv. oryzae PXO99A NC_010717 1 0 5-azacytidine-resistant derivative of PXO99, isolated in Los Ba¿os and classified as Philippine race 6 Plant/agriculture-associated 95754 Xenorhabdus bovienii SS-2004 NC_013892 1 0 nematodes (roundworms) Steinernema species Insect-associated/other symbiont Xenorhabdus nematophila ATCC 19061 NC_014228,NC_014170 1 1 acquired from American Type Culture Collection nematode Insect-associated/other symbiont 24446 Xylanimonas cellulosilytica DSM 15894 NC_013530,NC_013531 1 1 Decaying tree in Salamanca Spain Plant/agriculture-associated 578 Xylella fastidiosa 9a5c NC_002488,NC_002489,NC_002490 1 2 pathogenic strain (8.1b) derived from a pathogenic strain (8.1b) isolated in 1992 in France that had come from infected twigs derived from the sweet orange strain Valencia in Brazil in the same year Plant/agriculture-associated 124301 Xylella fastidiosa M12 NC_010513 1 0 almond trees in Kern County in the San Joaquin Valley of California Plant/agriculture-associated 85937 Xylella fastidiosa M23 NC_010577,NC_010579 1 1 almond tree isolated from an almond tree in California and is being sequenced for comparative analysis with other Plant/agriculture-associated bacteria Plant/agriculture-associated 171671 Xylella fastidiosa subsp. fastidiosa GB514 NC_017562,NC_017561 1 1 Texas grape Plant/agriculture-associated 71109 Xylella fastidiosa Temecula1 NC_004556,NC_004554 1 1 naturally infected Californian grapevine isolated in 1998 from a naturally infected Californian grapevine Plant/agriculture-associated 11519 Yersinia enterocolitica subsp. enterocolitica 8081 NC_008800,NC_008791 1 1 human septicaemia isolate Clinical/Human-associated 184081 Yersinia enterocolitica subsp. palearctica 105.5R(r) NC_015224,NC_015475 1 1 Chinese patient Clinical/Human-associated 176226 Yersinia enterocolitica subsp. palearctica Y11 NC_017564,NC_017565 1 1 humans and asymptomatic slaughter pigs stool of a human patient Clinical/Human-associated 191978 Yersinia pestis A1122 NC_017168,NC_017169,NC_017170 1 2 isolated from a California ground squirrel (Spermophilus beecheyi) in California in 1939 Terrestrial-animal-associated 97331 Yersinia pestis Angola NC_010159,NC_010158,NC_010157 1 2 deep-rooted isolate isolated prior to 1985 and belongs to the antiqua biovar Terrestrial-animal-associated 1796 Yersinia pestis Antiqua NC_008150,NC_008121,NC_008122,NC_008120 1 3 soil sample from the Republic of Congo isolated from a soil sample from the Republic of Congo, is being sequenced for comparative genome analysis of Yersinia pestis strains isolated from different parts of the world soil 3863 Yersinia pestis biovar Medievalis str. Harbin 35 NC_017265,NC_017263,NC_017266,NC_017264 1 3 human isolate from China Clinical/Human-associated 99487 Yersinia pestis biovar Microtus str. 91001 NC_005810,NC_005813,NC_005814,NC_005815,NC_005816 1 4 Microtus brandti plague focus of the Xilin Gol Grassland isolated from a Microtus-related plague focus Terrestrial-animal-associated 7843 Yersinia pestis CO92 NC_003143,NC_003131,NC_003132,NC_003134 1 3 patient who died of pneumonic plague after acquiring the disease from an infected cat isolated in the USA from a patient who died of pneumonic plague after acquiring the disease from an infected cat Clinical/Human-associated 77623 Yersinia pestis D106004 NC_017154,NC_017156,NC_017153,NC_017155 1 3 new plague focus Isolated from Apodemus chevrieri in Yulong County in 2006. Terrestrial-animal-associated 93679 Yersinia pestis D182038 NC_017160,NC_017159,NC_017157,NC_017158 1 3 Apodemus chevrieri (Chevrier's field mouse) isolated from Apodemus chevrieri (Chevrier's field mouse) in Yunnan province, China Terrestrial-animal-associated 65053 Yersinia pestis KIM 10 NC_004088,NC_004838 1 1 Clinical/Human-associated 46733 Yersinia pestis Nepal516 NC_008149,NC_008118,NC_008119 1 2 soil sample from Nepal isolated from a soil sample from Nepal, is being sequenced for comparative genome analysis of Yersinia pestis strains isolated from different parts of the world soil 122972 Yersinia pestis Pestoides F NC_009381,NC_009378,NC_009377 1 2 "Atypical strain isolated from the former Soviet Union. from natural foci located in the Transcaucasian highland, in the Mountain Altai and Transbikalian regions" Terrestrial-animal-associated 97410 Yersinia pestis Z176003 NC_014029,NC_014022,NC_014017,NC_014027 1 3 dead marmot isolated from a dead marmot in Tibet Autonomous Region, China Terrestrial-animal-associated 15693 Yersinia pseudotuberculosis IP 31758 NC_009708,NC_009705,NC_009704 1 2 the stools of a patient presenting with scarlet-like fever isolated in 1966 from the stools of a patient presenting with scarlet-like fever in the Primorski region of the former USSR Clinical/Human-associated 22266 Yersinia pseudotuberculosis IP 32953 NC_006155,NC_006154,NC_006153 1 2 human patient isolated from a human patient Clinical/Human-associated 20639 Yersinia pseudotuberculosis PB1/+ NC_010634,NC_010635 1 1 unknown 127545 Yersinia pseudotuberculosis YPIII NC_010465 1 0 unknown 36047 Zobellia galactanivorans Dsij NC_015844 1 0 Algae were collected in the English Channel near Roscoff (Brittany, France) Isolated in Roscoff (Brittany, France) from the red alga Delesseria sanguinea, 2001 Plant/agriculture-associated 130839 Zunongwangia profunda SM-A87 NC_014041 1 0 Deep-sea sediment; China, East China Sea, southern Okinawa Trough area Aquatic-environment 74099 Zymomonas mobilis subsp. mobilis ATCC 29191 NC_018145,NC_018146,NC_018147,NC_018148 1 3 Isolated in Kinshasa, Congo, from palm wine fermentations. Fermenting Elaeis palm sap Food-associated 135463 Zymomonas mobilis subsp. mobilis NCIMB 11163 NC_013355,NC_013358,NC_013356,NC_013357 1 3 Spoiled Bristish beer Food-associated 102260 Zymomonas mobilis subsp. mobilis ZM4 NC_006526 1 0 fermenting sugarcane juice isolated from fermenting sugarcane juice and is wild-type and unable to utilize xylose Food-associated 12943 Zymomonas mobilis subsp. pomaceae ATCC 29192 NC_015709,NC_015715,NC_015716 1 2 isolated in Bristol, United Kingdom, as a cider sickness-causing organism Sick cider, Bristol, England Food-associated