Salmonella enterica subsp. enterica serovar Choleraesuis
a patient with sepsis
Wolbachia wBm
Brugia malayi
Shigella dysenteriae Sd197
China
Shigella boydii Sb227
Shigella sonnei Ss046
epidemics
Carboxydothermus hydrogenoformans
Kunashir Island, Russia
a hot spring
Thermoanaerobacter tengcongensis MB4(T)
freshwater hot springs
Symbiobacterium thermophilum IAM 14863
compost
Hahella chejuensis
the coastal marine sediment
the southernmost island in Korea
Rickettsia bellii RML369-C
vegetation near Fayetteville, Arkansas
embryonated chicken eggs from a triturated pool of unfed adult Dermacentor variabilis ticks
Helicobacter acinonychis
Large felines
a biopsy of a Russian circus lion with gastroenteritis
Helicobacter pylori 26695
human
Helicobacter pylori J99
Haloquadratum walsbyi DSM 16790
solar saltern
Spain
Borrelia garinii PBi
a German patient with neuroborreliosis
Borrelia afzelii (FLI)
human skin
Escherichia coli K-12 W3110
the stool of a convalescent diphtheria patient
Yersinia enterocolitica subsp. enterocolitica 8081
a human septicaemia
Arthrobacter aurescens
soil at an atrazine spill site
South Dakota
soil
South Dakota spill site containing 1,000 lb of the herbicide atrazine
Neisseria meningitidis FAM18 (serogroup C)
the cerebrospinal fluid of a child suffering from meningitis
North Carolina
Streptococcus suis 98HAH33
Jiangsu, China
Streptococcus suis 05ZYH33
Sichuan, China
fatal cases of streptococcal toxic shock syndrome
Herminiimonas arsenicoxydans
the activated sludge
Mycoplasma agalactiae PG2
a goat
Minibacterium massiliensis
0.22-μm filtered water used for patients
the ultrapure water production and distribution system
Bacillus pumilus
the Jet Propulsion Lab (Pasadena, CA)
Deinococcus geothermalis
a hot pool
the Termi di Agnano, Naples, Italy
Italy
Francisella tularensis subsp. tularensis WY96-3418
a human finger wound
Staphylococcus aureus RF122
bovine mastitis
Clostridium botulinum A ATCC 19397
the western US
foodborne botulism cases
Clostridium botulinum A2 Kyoto
an infant botulism case
Japan
Clostridium botulinum A3 Loch Maree
a food poisoning incident
Scotland
Clostridium botulinum Ba4 657
Texas
Clostridium botulinum B1 Okra
the National Institute of Health
Staphylococcus aureus subsp. aureus USA300_TCH1516 (CA-MSSA)
San Francisco
Texas Children's Hospital in Houston
Staphylococcus aureus subsp. aureus USA300_FPR3757, community-acquired meticillin-resistant
an abscess of an HIV-positive intravenous drug user
healthy pediatric patient
an adolescent patient with severe sepsis syndrome
Texas Children's Hospital
pediatric patients
Leptospira biflexa serovar Patoc Patoc 1 (Paris)
stream water
Leptospira biflexa serovar Patoc Patoc 1 (Ames)
Acinetobacter baumannii SDF
louse
Acinetobacter sp. ADP1
Acinetobacter baumannii AYE
body lice
Shewanella piezotolerans WP3
deep-sea sediment
Shewanella oneidensis MR-1
Oneida Lake
NY, USA
Lake sediments
western Pacific Ocean
sediment
a shallow sediment sample
the western Pacific Ocean (E142°30′08″, N8°00′11″)
Shewanella loihica PV-4
the South Rift of Loihi Seamount, Hawaii
iron-rich microbial mats at an active, deep-sea, hydrothermal Naha vent
Anaeromyxobacter dehalogenans 2CP-C
pristine soils
Brucella abortus S19
the milk of American Jersey Cattle
Saccharophagus degradans
the Chesapeake Bay watershed
decaying salt marsh cord grass, Spartina alterniflora
Francisella tularensis subsp. holarctica LVS (Live Vaccine Strain)
live vaccine
Francisella tularensis subsp. tularensis SCHU S4
Psychromonas ingrahamii
the Arctic
sea ice
the ice column
Colwellia psychrerythraea 34H
Idiomarina loihiensis L2TR
Treponema pallidum subsp. pallidum SS14
Atlanta
a patient with secondary syphilis
Treponema pallidum subsp. pallidum Nichols
cerebrospinal fluid of the patient with neurosyphilis
Washington, D.C.
Bifidobacterium longum DJO10A
a healthy young adult's feces
Xanthomonas oryzae pv. oryzae PXO99A
Los Baños
Mycobacterium tuberculosis H37Ra
virulent strain H37
Mycobacterium tuberculosis H37Rv, laboratory strain
a 19 year-old male patient with chronic pulmonary tuberculosis
Azorhizobium caulinodans
stem nodules
Klebsiella pneumoniae 342
the interior of nitrogen-efficient maize plants
nitrogen-efficient Zea mays L. cv. CIMMYT 342
Methylacidiphilum infernorum
the Hell's Gate geothermal area
the Hell's Gate geothermal area in New Zealand
New Zealand
the North Island of New Zealand
Hell's Gate (Tikitere)
a soil sample
methane-emitting geothermally heated soil
Wolbachia pipientis
Culex pipiens mosquitoes
Streptococcus equi subsp. zooepidemicus MGCS10565
the state of Minas Gerais, Brazil
Brazil
the throat of a patient with nephritis who was diagnosed during an epidemic of this disease
Borrelia duttonii
Ethiopia
an adult patient with louse-borne relapsing fever
Borrelia recurrentis
Tanzania
a 2-year-old girl with tick-borne relapsing fever
Phenylobacterium zucineum
human erythroleukemia cell line K562
the human leukemia cell line K562
Aeromonas salmonicida
the Eure river, France
France
a brown trout
Orientia tsutsugamushi Ikeda
patient
Niigata Prefecture, Japan
Streptococcus pneumoniae ST556
a patient with otitis media
Vibrio cholerae M66-2
Makassar
Escherichia coli O152:H28 SE11 (commensal)
a Healthy Adult
feces of a healthy adult
feces collected from a healthy adult human
Anoxybacillus flavithermus
the waste water drain
the Wairakei geothermal power station in New Zealand
Thermomicrobium roseum
an alkaline siliceous hot spring
Yellowstone National Park
Toadstool Spring
Toadstool Spring in Yellowstone National Park
Escherichia coli O17:K52:H18 UMN026 (ExPEC)
a woman with uncomplicated acute cystitis
the USA (Minnesota)
Escherichia coli O45:K1:H7 S88 (ExPEC)
the cerebro-spinal fluid of a new born with late-onset neonatal meningitis
Cerebro-spinal fluid
Escherichia coli O8 IAI1 (commensal)
the faeces of a young healthy military conscript
Escherichia coli O81 ED1a (commensal)
the faeces of a healthy man
Escherichia coli 55989 (EAEC)
the diarrheagenic stools of an HIV-positive adult suffering from persistent watery diarrhea
Central African Republic
Escherichia coli O7:K1 IAI39 (ExPEC)
the urine of a patient with pyelonephritis
Acidithiobacillus ferrooxidans ATCC 23270
Aliivibrio salmonicida LFI1238
the head kidney (lymphoid organ)
the northern parts of Norway
Norway
cod
Nautilia profundicola
hydrothermal vents
13°N along the East Pacific Rise Axial Caldera
the biomass of an Alvinella pompejana episymbiont community
various mats on vent chimneys
a deep-sea hydrothermal vent
Loihi, Hawaii
hydrothermal vent
Vent
Nitratiruptor sp. SB155-2
Psychromonas ingrahamii 37
polar sea ice
deep-sea hydrothermal vents
Stenotrophomonas maltophilia K279a
the Bristol Oncology Unit, Bristol, UK
an elderly male patient undergoing chemotherapy
a blood sample taken shortly before death
Lactobacillus fermentum IFO 3956
fermented plant material
Lactobacillus reuteri JCM 1112
human feces
Laribacter hongkongensis
the blood and thoracic empyema of an alcoholic liver cirrhosis patient
Hong Kong
drinking water reservoirs
the blood and empyema pus of a patient
Streptococcus equi subsp. zooepidemicus H70
a nasal swab taken from a healthy Thoroughbred racehorse
Streptococcus equi subsp. equi 4047
the New Forest, England
a horse with strangles
Newmarket, England
a human case of nephritis that was part of a severe epidemic
Staphylococcus aureus subsp. aureus 71193
northern Manhattan, New York, NY, USA
Salmonella enterica subsp. enterica serovar Paratyphi A AKU12601
a Pakistani paratyphoid patient
Karachi, Pakistan
Pakistan
Deinococcus deserti
hot, arid desert surface sand
Sahara
surface sand
Deinococcus geothermalis DSM 11300
the Sahara
upper sand layers
the surface sand
Staphylothermus marinus
volcanically heated sediments
a black smoker
Streptococcus pneumoniae CGSP14 (serotype 14)
Chang Gung Memorial Hospital and Children's Hospital, Taoyuan, Taiwan
patients with bacteremic pneumonia treated
a child with necrotizing pneumonia, simultaneously complicated with hemolytic uremic syndrome
Methylobacterium extorquens DM4
Switzerland
industrial wastewater sludge
Methylobacterium extorquens AM1
an airborne contaminant growing on methylamine
Oxford, England
Methanocorpusculum labreanum
tar pit sediments
Methanospirillum hungatei JF-1
sewage sludge
Francisella tularensis subsp. mediasiatica FSC147
the Alma-Ata region of Kazakhstan
Kazakhstan
the rodent species Meriones meridianus (Midday gerbil)
Chlamydia trachomatis Sweden2
Malmo, Southern Sweden
Sweden
Genital tract
Chlamydia trachomatis B/TZ1A828/OT
ocular
Chlamydia trachomatis B/Jali20/OT
Rickettsia africae
the Shulu province of Ethiopia
an Amblyomma variegatum tick collected from cattle
Mycobacterium abscessus ATCC 19977
a human knee infection with subcutaneous abscess-like lesions
Bartonella grahamii
the vicinity of Uppsala in central Sweden
wood mouse
Teredinibacter turnerae
the gills of a broad range of wood-boring marine bivalves of the family Teredinidae (shipworms)
the shipworm Bankia gouldi
shipworm
the Newport River Estuary, Beaufort North Carolina
a specimen of the shipworm Bankia gouldi
Saccharophagus degradans 2-40
decaying sea grass (Spartina alterniflora)
Candidatus Hodgkinia cicadicola
the cicada Diceroprocta semicincta
cicadas
Streptococcus suis SC84
Streptococcus suis BM407
Streptococcus suis P1/7
pigs
Vietnam
Europe
a human case of meningitis
Ho Chi Minh City, Vietnam
Sichuan Province, China
a case of streptococcal toxic shock-like syndrome
an ante-mortem blood culture from a pig dying with meningitis
a case of human meningitis
Vibrio fischeri MJ11
the North Pacific Ocean
the Japanese pinecone fish, Monocentris japonica11
a live M. japonica
the Steinhart Aquarium
Photorhabdus asymbiotica
North America
the blood of an 80 year old female patient with endocarditis
Maryland, USA
Photorhabdus luminescens subsp. laumondii TTO1
Trinidad and Tobago
entomopathogenic nematode vector collected from soil
a female patient with endocarditis
vector nematode
nematode vector, collected by baiting soil with insects
an 80-year-old female patient with endocarditis
Maryland
Thermococcus gammatolerans
hydrothermal chimneys
the mid-Atlantic Ridge and at the Guyamas basin
Pseudomonas fluorescens SBW25
the University Farm, Wytham, Oxford, UK
the leaf surface of a sugar beet plant
Pseudomonas fluorescens Pf0-1
Sherborn, Massachusetts, USA
loam soil
bulk loam soil
the leaf surfaces of a sugar beet plant
Francisella tularensis subsp. holarctica FTNF002-00
the first known clinical case of bacteremic F. tularensis pneumonia
an immunocompetent individual
Southern Europe
an immunocompetent 56-year old male with bacteremic F.t. holarctica pneumonia
Brucella microti
red foxes
Lower Austria
Austria
Rhodoferax ferrireducens
subsurface sediments
Oyster Bay, VA
Neorickettsia risticii
horses with Potomac horse fever
Blattabacterium sp. (Blattella germanica)
the fat body of B. germanica females
Neisseria meningitidis 8013 (serogroup C)
the Institut Pasteur
the blood of a 57-year-old male
Bifidobacterium dentium
dental caries
human dental caries
Rickettsia peacockii
Ixodes scapularis cell line ISE6
Escherichia coli O157:H7 EDL933 (EHEC)
the University of Maryland
Escherichia coli O55:H7 CB9615 (EPEC)
Germany
an infant with diarrhea
Escherichia coli O44:H18 042 (EAEC)
a child with diarrhea in the course of an epidemiologic study
Lima, Peru
Peru
Pseudomonas aeruginosa PA7
Argentina
Xanthomonas albilineans
Guadeloupe
Xanthomonas campestris pv. campestris ATCC 33913
cabbage
Xanthomonas oryzae pv. oryzae MAFF 311018
rice
Stenotrophomonas maltophilia R551-3
poplar
Xylella fastidiosa 9a5c
citrus
Xanthomonas citri pv. citri 306 (Xanthomonas axonopodis pv. citri 306)
the blood of an infected patient
Xanthomonas campestris pv. vesicatoria 85-10
pepper
Xylella fastidiosa Temecula1
grapevine
a diseased stalk of sugarcane cv. H63-1418
Methanobrevibacter ruminantium
bovine rumen contents
Francisella tularensis subsp. tularensis NE061598
Nebraska, United States of America
United States of America
a human with clinical disease
Ohio
Francisella tularensis subsp. tularensis FSC198
Slovakia
Nebraska
the blood of a patient with ulceroglandular tularemia
Corynebacterium aurimucosum
a vaginal swab of a woman with spontaneous abortion
a vaginal swab of a 34-year-old woman who experienced a spontaneous abortion during month six of pregnancy
a vaginal swab of a 34-year-old female who experienced a spontaneous abortion during month six of pregnancy
a female who presented with the sudden onset of premature labor during month six of gestation
the urogenital tract of a 34-year-old woman who experienced a spontaneous abortion during month six of pregnancy
Candidatus Sulcia muelleri DMIN
the bacteriome of the green sharpshooter Draeculacephala minerva
the green sharpshooter (GSS) Draeculacephala minerva Ball
the green sharpshooter bacteriome
the sharpshooter bacteriome metasample
sharpshooters
California
Legionella pneumophila 2300/99 Alcoy
a patient
Alcoy (Spain)
sputum of a patient with Legionnaires’ disease
Cupriavidus metallidurans
a metal processing factory
Deferribacter desulfuricans SSM1
a hydrothermal vent chimney
deep-sea hydrothermal vent chimneys
a deep-sea hydrothermal vent chimney
the Suiyo Seamount in the Izu-Bonin Arc, Japan
Rhodospirillum centenum
Wyoming, United States
hot spring mud
Brachyspira pilosicoli 95/1000
Western Australia
Australia
the diarrheic feces of a commercial pig with porcine intestinal spirochetosis
Staphylococcus aureus subsp. aureus ST398 (MRSA)
a case of human endocarditis
a human case of endocarditis
a blood culture of a 63 year old female patient with endocarditis of the mitral valve proven by detection of vegetations and an abscess visible on a transoesophageal echocardiogram
Ralstonia solanacearum GMI1000
Asia
Ralstonia solanacearum PSI07
Indonesia
Ralstonia solanacearum CFBP2957
the Americas
Ralstonia solanacearum CMR15
Africa
tomato
tomato plants
Tomato
Guyana
tomato plants (Solanum lycopersicum)
the French West Indies
Cameroon
French West Indies
Bacillus cereus biovar anthracis CI
a chimpanzee that had died with clinical symptoms of anthrax
the rainforest of the Taï National Park, Côte d'Ivoire
Côte d'Ivoire
deceased wild chimpanzees
Bacillus cereus E33L (zebra killer)
a dead zebra suspected to have died of anthrax
Bacillus thuringiensis 97-27 (serovar konkukian)
a case of severe human tissue necrosis
Streptococcus mutans NN2025
Streptococcus mutans UA159 (serotype C)
the United States
a patient with dental caries
Streptococcus mutans LJ23 (serotype k)
Japanese
Dechloromonas aromatica
soil environments
Potomac River
sludge contaminated with benzene, toluene, ethylbenzene and xylene compounds
Butyrivibrio proteoclasticus
the bovine rumen
Campylobacter jejuni subsp. jejuni 81116
Campylobacter jejuni RM1221
chicken
Campylobacter jejuni subsp. jejuni M1
the diarrheic stools of one research team member 9 days after visiting a poultry processing plant
Escherichia coli ABU 83972
a young girl, who was colonized for more than three years
a girl with asymptomatic bacteriuria
the urinary tract of a schoolgirl
Helicobacter pylori P12
a duodenal ulcer patient
Helicobacter pylori Shi470
residents
the remote Peruvian Amazonian village of Shimaa
the village of Shimaa in the remote Peruvian Amazon
gastric biopsy specimens from residents
Shimaa village
Shimaa, ## ## village in the remote Peruvian Amazon
gastric biopsies from 44 residents
an antrum biopsy of a 24-year old female with moderate chronic gastritis
Staphylococcus aureus subsp. aureus ED133
Ruminant
Staphylococcus aureus RF122/ET3-1, bovine mastitis-causing
Ireland
Staphylococcus aureus subsp. aureus N315, hospital-acquired meticillin-resistant, vancomycin-susceptible
Staphylococcus aureus subsp. aureus Mu50, MRSA strain with vancomycin-intermediate resistance
Staphylococcus aureus subsp. aureus Mu3, MRSA strain with heterogeneous vancomycin-intermediate resistance
Staphylococcus aureus subsp. aureus Newman
Staphylococcus aureus subsp. aureus MW2, community-acquired MRSA
Human
Staphylococcus aureus subsp. aureus MRSA252, methicillin-resistant
Staphylococcus aureus subsp. aureus MSSA476, methicillin-susceptible
bovine
Staphylococcus aureus subsp. aureus JH9, meticillin-resistant, vancomycin-resistant
Staphylococcus aureus subsp. aureus COL, methicillin-resistant
ovine
Corynebacterium pseudotuberculosis FRC41
a 12-year-old girl with necrotizing lymphadenitis
the inguinal lymph node of a 12-year-old girl with necrotizing lymphadenitis
the inguinal lymph node of a 12-year-old French girl with necrotizing lymphadenitis
a rare case of necrotizing lymphadeniti
Escherichia coli W
the soil of a cemetery
near Rutgers University
Brachybacterium faecium
the poultry deep litter
Pedobacter heparinus
dry soil
Actinosynnema mirum
the Raritan River, New Jersey.
Jersey
a grass blade
Desulfomicrobium baculatum
water-saturated manganese carbonate ore
Acidimicrobium ferrooxidans DSM 10331
the Krísuvík geothermal area, Iceland
Iceland
hot springs
Leptotrichia buccalis
wet mounts of tooth scrapings
Tar Pit Lake at the La Brea Tar Pits in Los Angeles
surface sediments
Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California
the La Brea Tar Pits
Capnocytophaga ochracea
a human oral cavity
Cryptobacterium curtum
a periodontal pocket sample of an adult patient
Anaerococcus prevotii
human plasma
Catenulispora acidiphila
a forest soil sample
Gerenzano, Italy
Dyadobacter fermentans
maize plants
plants
Saccharomonospora viridis
peat-bog
geothermally heated sediments
Vulcano, Italy
Jonesia denitrificans
cooked ox blood
Pirellula staleyi
the freshwater
Lake Lansing, MI, USA
Rhodothermus marinus DSM 4252
marine hot springs
a submarine hot spring
Halomicrobium mukohataei
Salinas Grandes in Jujuy, Andes highlands, Argentina
Thermanaerovibrio acidaminovorans
The Netherlands
Netherlands
an anaerobic reactor of a sugar refinery
Streptobacillus moniliformis
a patient with rat bite fever
Desulfotomaculum acetoxidans
piggery waste
Göttingen, Germany
Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
a hot and acidic spring
Yellowstone National Park, USA
Xylanimonas cellulosilytica
Salamanca, Spain
a decayed tree, Ulmus nigra
Haliangium ochraceum
a dry seaweed sample (Laminariales)
Desulfohalobium retbaense
Retba Lake in Senegal
Senegal
sediments of the hypersaline ## lake
surface sediments of the hypersaline ## lake
Retba Lake in Senegal (Western Africa)
Rhizobium leguminosarum bv. trifolii WSM2304
Uruguay
Trifolium polymorphum
Glencoe Research Station near Tacuarembó, Uruguay
a nodule recovered from the roots of the perennial clover Trifolium polymorphum
Chitinophaga pinensis
Alderley, Brisbane, Australia
an infusion of litter from the base of a pine tree
Sinorhizobium medicae
Medicago murex root nodule
Sardinia, Italy
south of Tempio in Sardinia
a nodule recovered from the roots of an annual medic (Medicago murex)
Veillonella parvula
human intestinal tract
Sphaerobacter thermophilus
an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge
München-Grosslappen, Germany
thermal treated municipal sewage sludge
Acetohalobium arabaticum
lagoons
the Arabat spit (East Crimea) which separates Sivash lake from the Sea of Azov
Acidaminococcus fermentans
the gastrointestinal tract
a pig alimentary tract
Ignisphaera aggregans
Kuirau Park, Rotorua, New Zealand
a near neutral, boiling spring
Meiothermus silvanus
the hot spring
Vizela in northern Portugal
Portugal
Sebaldella termitidis
intestinal content of Mediterranean termites
posterior intestinal content of Reticulitermes lucifugus (Mediterranean termites)
Segniliparus rotundus
human sputum
Tennessee, USA
Conexibacter woesei
temperate forest soil
Gerenzano (Italy)
a contaminant of a Dactylosporangium colony
a soil
Thermocrinis albus
whitish streamers
Hveragerthi, Iceland
Geodermatophilus obscurus
the Amargosa Desert of Nevada, USA
Sulfurospirillum deleyianum
near Heinigen, Braunschweig area, Germany
anoxic mud of a forest pond
Archaeoglobus profundus
marine hydrothermal habitats
a deep sea hot vent area
Guaymas, Mexico
Mexico
marine hydrothermal systems
Coraliomargarita akajimensis
seawater surrounding the hard coral Galaxea fascicularis
Majanohama, Akajima, Okinawa, Japan
Opitutus terrae PB90-1
a rice paddy soil microcosms
Brachyspira murdochii
the intestinal content of a healthy swine
Canada
a healthy swine
Arcobacter nitrofigilis
Spartina alterniflora Loisel
roots of Spartina alterniflora Loisel (cordgrass)
the East coast of Canada
Thermobispora bispora
decaying manure
Berlin (Germany)
Denitrovibrio acetiphilus
a representative of a population reducing nitrate to ammonia in a laboratory column simulating the conditions in off-shore oil recovery fields.
a laboratory model column simulating marine anoxic mineral oil reservoir conditions
marine medium with acetate
Rhizobium leguminosarum bv. trifolii WSM1325
the Greek Island of Serifos
root nodules
a nodule recovered from the roots of an annual clover plant
near Livadi beach on the Greek Cyclades island of Serifos
Desulfarculus baarsii
near the University of Konstanz, Germany
a ditch sediment
a ditch near the University of Konstanz, Germany
anoxic mud
Methanothermus fervidus
an anaerobic Icelandic spring
Ilyobacter polytropus
Cuxhaven, Germany
marine anoxic mud
Syntrophothermus lipocalidus
granular sludge
Thermaerobacter marianensis
the western Pacific Ocean (Mariana Trench)
a mud sample of the Challenger Deep
the Challenger Deep in the Mariana Trench
Intrasporangium calvum
a school dining room
plates of meat-peptone agar
Thermobaculum terrenum
a slightly acidic extreme thermal soil
Yellowstone National Park, Wyoming (USA)
a moderately acidic (pH 3.9) extreme thermal soil
Yellowstone National Park (YNP), Wyoming (USA)
Ferrimonas balearica
the upper few centimeters of marine sediment
the Palma de Mallorca harbor, Spain
Vulcanisaeta distributa
Ohwakudani, Kanagawa, Japan
Spirochaeta smaragdinae
a Congo offshore oilfield
Congo
an oil-injection production water sample
Thermosediminibacter oceani
a core sample of deep sea sediments
a core sediment sample
Sulfurimonas autotrophica
the Hatoma Knoll in the Mid-Okinawa Trough hydrothermal field
the surface of a deep-sea hydrothermal sediment
Bartonella clarridgeiae
Cat
cats
Clostridium acetobutylicum EA 2018
Mycoplasma mycoides subsp. capri LC 95010
a young female goat (alpine breed) with polyarthritis
near Bourges (France)
Bacillus atrophaeus
archival spore suspensions in sterile soilfrom
the University of Wisconsin
sterile soil
Paludibacter propionicigenes
Yamagata, Japan
rice plant residues in an anoxic rice-field soil
Desulfobulbus propionicus
a village ditch in Lindhorst near Hannover
anaerobic mud
Bacteroides helcogenes
a pig abscess
Calditerrivibrio nitroreducens
Yumata, Nagano, Japan
hot-spring water
Corynebacterium pseudotuberculosis 1002
goats
Corynebacterium pseudotuberculosis C231
sheep
an ovine host
a caprine host
Candidatus Caldiarchaeum subterraneum
a geothermal water stream
Candidatus Liberibacter solanacearum
potato psyllids
potato psyllids (Bactericera cockerelli Sulc)
potato fields in Dalhart, Texas, USA
Bacteroides fragilis 638R
the USA
Bacteroides fragilis YCH46
Bacteroides fragilis NCTC9343
the UK
Chicago, USA
London (UK)
peritoneal infection
Yamaguchi ## Japan
a blood culture
Chicago
Yamaguchi Prefecture (Japan)
St Bartholomew’s Hospital, London, UK
an abdominal infection
an abdominal abscess
Helicobacter pylori B8
H. pylori strain B128
the human isolate B128
Helicobacter pylori B38
a 62-year-old man suffering from mucosa-associated lymphoid tissue lymphoma
the gastric antrum of an Amerindian resident
a remote Amazonian village in Peru
Neisseria lactamica
a six-week-old child
Escherichia coli O83:H1 NRG 857C
the ileum of a Crohn's Disease patient
the terminal ileum of a patient with Crohn's Disease
a biopsy of a Crohn's disease patient
the Charite Hospital, Germany
Clostridium botulinum BKT015925
poultry broilers
Klebsiella pneumoniae subsp. rhinoscleromatis SB3432
cases of rhinoscleroma
tissue culture, nasal swabs or blood culture
a biopsy of the left nasal cavity of an 11-year old patient diagnosed with rhinoscleroma
the Avicenne hospital, Bobigny, France
Treponema paraluiscuniculi
an infected rabbit
Haloquadratum walsbyi C23
saltern crystallizer ponds
Haloquadratum walsbyi DSM 16790 (HBSQ001)
Helicobacter pylori F32
Fukui, Japan
Helicobacter pylori F57
Homo sapiens
Helicobacter pylori F16
Helicobacter pylori F30
patients with ## ## ## ## intestinal type gastric cancer
patients with diffuse type gastric cancer
patients with ## ## ## ## ## ## ## ## duodenal ulcer
patients with ## ## ## ## ## ## ## ## ## ## ## gastritis
Helicobacter pylori 52
Korea
Helicobacter pylori 51
Mycoplasma bovis Hubei-1
a Chinese farm
calf pneumonia
Mycoplasma gallisepticum S6
Acholeplasma laidlawii PG-8A
Roseobacter litoralis Och 149
seaweed
Roseobacter denitrificans OCh 114
marine seaweed
Brucella pinnipedialis
marine mammals
Lactococcus garvieae Lg2
yellowtail
Lactococcus garvieae ATCC 49156
diseased yellowtail
Hippea maritima
Matipur Harbor, Papua New Guinea
Papua New Guinea
shallow-water hot vents
Pyrolobus fumarii
a black smoker wall
TAG site, Mid Atlantic Ridge
Halanaerobium praevalens
the hypersaline surface sediments
Great Salt Lake, Utah, USA
Nitratifractor salsuginis
the Iheya North hydrothermal field in the Mid-Okinawa Trough in Japan
Iheya North
a deep-sea hydrothermal vent chimney at the summits of the sulfide mounds in the sediment-hosted back-arc hydrothermal system
Haliscomenobacter hydrossis
Mahella australiensis
the Riverslea Oil Field
the Bowen-Surat basin in Queensland, eastern Australia
Desulfobacca acetoxidans DSM 11109
sludge
granular sludge of a laboratory-scale upflow anaerobic sludge bed (UASB) reactor
Treponema succinifaciens
Corynebacterium ulcerans 809
Corynebacterium ulcerans BR-AD22
a nasal sample of an asymptomatic dog
the metropolitan area of Rio de Janeiro
an elderly woman with fatal pulmonary infection
animal specimens
a bronchoalveolar lavage (BAL) sample of an 80-year-old woman with rapidly fatal pulmonary infection and a history of chronic bilateral limb ulcers
a nasal sample of a 5-year-old female dog
an animal shelter in the metropolitan area of Rio de Janeiro
an asymptomatic dog
a patient with pulmonary infection
a nasal sample of an asymptomatic female dog
a bronchoalveolar lavage sample of an elderly woman with a fatal pulmonary infection and a history of leg skin ulcers
Rio de Janeiro
a human clinical source
a human clinical specimen
the nares of an asymptomatic dog
animal reservoirs
clinical specimens
animal
Ramlibacter tataouinensis
a semi-arid region
South Tunisia (Tataouine)
Tunisia
a sandy soil of a semi-arid region
Staphylococcus aureus subsp. aureus MSHR1132
northern Australia
the Royal Darwin Hospital (RDH), Darwin, Northern Territory, Australia
the blood culture of an indigenous woman with necrotizing fasciitis
Thermoproteus tenax
a solfatare
Pseudomonas aeruginosa M18
sweet melon rhizosphere
Shanghai suburb
the sweet melon rhizosphere
Micavibrio aeruginosavorus ARL-13
wastewater
sewage water
Escherichia coli clone D i2
Escherichia coli clone D i14
dog
faecal samples
the dog
Corynebacterium variabile
the surface of smear-ripened cheeses
the smear-ripened cheese Gubbeen
the surface of an Irish farmhouse smear-ripened cheese
Streptococcus suis D9
Streptococcus suis ST1
Streptococcus suis D12
Streptococcus suis SS12
Lactobacillus ruminis
the bovine
cows
Lactobacillus sanfranciscensis
an industrial sourdough fermentation
a commercial mother sponge with a tradition of continuous propagation
Thermus scotoductus
a South African gold mine
South Africa
fissure water collected 3.2 km below surface in a South African gold mine
water collected more than 3 kilometers underground
Mycobacterium gilvum Spyr1
Greece
a creosote contaminated site
a creosote polluted site
Perivleptos, ## ## ## ## in Epirus, Greece (12 Km North of the city of Ioannina)
Taylorella asinigenitalis MCE3
the genital tract of a 6-year-old donkey jack
a stud farm in the Loir-et-Cher, France
Treponema pallidum subsp. pertenue SamoaD
Western Samoa
Samoa
Treponema pallidum subsp. pertenue Gauthier
Brazzaville, Congo
Treponema pallidum subsp. pertenue CDC2
Akorabo, Ghana
Ghana
Mycobacterium africanum
The Gambia
Gambia
a 27 year old HIV uninfected male patient with 3+ smear positive pulmonary tuberculosis
northern Manhattan
humans
patients with S. aureus infections
skin and soft tissue infections
Desulfitobacterium hafniense DCB-2
a municipal sludge
Denmark
Desulfitobacterium hafniense Y51
a Japanese soil contaminated with tetrachloroethene
Haemophilus influenzae F3047 (nontypeable)
Haemophilus influenzae 86-028NP (nontypeable)
middle ear secretions from patients with otitis media
Haemophilus influenzae R2866 (nontypeable)
a child with meningitis
Haemophilus influenzae R2846 (nontypeable)
Vibrio cholerae O1 2010EL-1786
clinical infections
Vibrio cholerae MJ-1236
Vibrio cholerae O395
Haiti
Vibrio cholerae O1 biovar El Tor N16961
Bangladesh
Matlab, Bangladesh
Deinococcus gobiensis
the cold Gobi desert
Deinococcus radiodurans R1
canned meat that had spoiled following exposure to X-rays
the upper sand layers of the cold Gobi desert
the Xinjiang region in China
canned meat
Deinococcus deserti VCD115
the hot Sahara desert
the Sahara desert
Truepera radiovictrix DSM 17093
the Island of Sao Miguel
hot spring runoff
Deinococcus maricopensis DSM 21211
the Sonoran Desert soil
Escherichia coli O157:H7 TW14359 (EHEC)
Escherichia coli O157:H7 Xuzhou21 (EHEC)
Escherichia coli O157:H7 Sakai (EHEC)
Xuzhou
human patients
an hemolytic uremic syndrome patient
USA
Methanosaeta harundinacea
an upflow anaerobic sludge blanket reactor
Beijing
our lab
upflow anaerobic sludge blanket reactor
Burkholderia pseudomallei 1026b
Sapprasithiprasong Hospital in Thailand
Thailand
a 29-year-old female patient with septicemic melioidosis with skin, soft tissue, spleen and joint involvement
blood
Ignavibacterium album
microbial mats associated with the sulfide-rich waters
Yumata Hot Spring
Mycoplasma bovis HB0801
Hubei, China
a lesioned bovine lung
lesioned lung tissue
Mycoplasma bovis PG45
cow mastitis milk
Hubei province
Yingcheng city in Hubei province, China
the lesioned lung of an infected beef cattle
America
the lesioned lung tissue
Chlamydia trachomatis E/SW3
Cervix
Chlamydia trachomatis L2b/Ams3
Chlamydia trachomatis L2b/Ams1
Chlamydia trachomatis L2b/Ams4
Chlamydia trachomatis L2b/Ams5
Chlamydia trachomatis L2b/Ams2
Chlamydia trachomatis L1/224
Chlamydia trachomatis L1/1322/p2
Chlamydia trachomatis L1/115
Chlamydia trachomatis A/363
Rombo, Northern Tanzania, 550km from Kongwa
England
a leaf of sugar beet
Pseudomonas fluorescens A506
a leaf surface
California, USA
Natrinema sp. J7-2
a salt mine
Hubei province, China
Natrialba magadii
Lake Magadi in Kenya
Kenya
Haloterrigena turkmenica DSM 5511
Turkmenistan
sulfate saline soil
Natronomonas pharaonis DSM 2160
a soda lake
Egypt
Corynebacterium ulcerans 0102
the pharyngeal pseudomembrane of a 52-year-old woman presenting with a sore throat and fever
a patient with a rapid fatal pulmonary infection
Enterococcus faecium DO
the blood of a patient with endocarditis
Bifidobacterium asteroides
the hindgut of Apis mellifera var. ligustica
Treponema pallidum subsp. pallidum Mexico A
an 18-year-old male, with primary syphilis
male, with primary syphilis
Listeria monocytogenes Clip81459 (serotype 4b)
person
Listeria monocytogenes L99
food
the Netherlands
Escherichia coli O104:H4 2009EL-2050
the Republic of Georgia
Georgia
Escherichia coli O104:H4 2009EL-2071
Escherichia coli O104:H4 2011C-3493
patients
a US patient with a history of travel to Germany
human stool
Geobacter sulfurreducens KN400
an anode poised at a very low potential
a fuel cell
Morganella morganii
postoperative care of a cancer patient with a gallbladder stone
the blood of a patient
blood of a 57-year-old man during postoperative care.
a porcine
Brachyspira pilosicoli B2904
an avian
Brachyspira pilosicoli WesB
a human
a chicken exhibiting clinical symptoms of avian intestinal spirochaetosis
an Australian Aboriginal child with diarrhoea
a pig with porcine intestinal spirochaetosis
the diarrhoeic faeces of a pig with porcine intestinal spirochaetosis
a chicken displaying clinical symptoms of avian intestinal spirochaetosis
an Australian child with diarrhoea
Bordetella pertussis 18323
Bordetella bronchiseptica MO149
Bordetella parapertussis Bpp5
human-isolated
Arthrobacter sp. Rue61a
sewage sludge able to utilize quinaldine (2-methylquinoline) as sole carbon and energy source
Arthrobacter sp. FB24
a microcosm that contained chromate, lead- and hydrocarbon-contaminated soils
the biological wastewater treatment plant of a coal tar refinery
Castrop-Rauxel, Germany
Melioribacter roseus
the Tomsk region of Russia
microbial mats
Ignavibacterium album JCM 16511
Yumata, Japan
a microbial mat
Propionibacterium acidipropionici
Bdellovibrio bacteriovorus Tiberius
the River Tiber
the River Tiber in Rome
an organically polluted and diversely-bacterially populated river
the River Tiber in Rome (41°53'59.82"N 12°27'50.19"E)
Pelobacter carbinolicus
Rhizobium tropici
Colombia
a common-bean nodule
Desulfovibrio piezophilus
wood falls
the Mediterranean deep-sea
Mediterranean deep-sea
Arcobacter butzleri 7h1h
cattle
the North West of England
Arcobacter butzleri RM4018
a clinically-ill human
Simiduia agarivorans
shallow coastal seawater
Chlamydia psittaci 01DC12
Swine
a pig
Saxony-Anhalt, Germany
Helicobacter heilmannii
the Gastric Mucosa of a Kitten with Severe Gastritis
Carnobacterium maltaromaticum
ripened soft cheese
a soft ripened cheese
Carnobacterium sp. 17-4
permanent cold seawater
Thermus thermophilus JL-18
the U.S. Great Basin
the Great Boiling Spring system
Thermus oshimai
Corynebacterium halotolerans
a saline soil
Xinjiang Province in western China
saline soil
Corynebacterium pseudotuberculosis P54B96
antelope
liver, lung and mediastinal lymph node lesions in an antelope
Tepidanaerobacter acetatoxydans Re1
ammonium-rich, mesophilic, methanogenic systems
Acinetobacter baumannii D1279779
the bacteraemic infection of an Indigenous Australian
a human body louse
the Royal Darwin Hospital
a bacteraemic infection of an indigenous Australian male
Lactobacillus brevis KB290
a traditional Japanese fermented vegetable
Mycoplasma hyopneumoniae 7422
an infected swine
Lindóia do Sul, Santa Catarina, Brazil
Staphylococcus lugdunensis N920143
a breast abscess
Wolbachia wPip, endosymbiont of Culex quinquefasciatus (mosquito)
Culex quinque-fasciatus
Wolbachia sp. wMel, endosymbiont of Drosophila melanogaster (fruit fly)
Drosophila melanogaster
the mosquito Culex quinquefasciatus
Wolbachia wBm, endosymbiont of Brugia malayi TRS
the nematode Brugia malayi
Wolbachia sp. wRi, endosymbiont of Drosophila simulans
Drosophila simulans
Wolbachia endosymbiont of Drosophila simulans wNo
Wolbachia endosymbiont of Drosophila simulans wHa
Hawaii and ## French Polynesia
French Polynesia
infected fly line
Hawaii
a series of backcrosses on a double-infected fly line
Noumea
Mycoplasma hyopneumoniae 168-L
an Er-hua-nian pig (a Chinese local breed very sensitive to M. hyopneumoniae) with typical clinical and pathogenic characteristics of mycoplasmal pneumonia of swine (MPS)
Treponema pallidum Fribourg-Blanc
baboons (Papio cynocephalus)
West Africa
Papio cynocephalus
Thermotoga maritima
geothermally heated marine sediment
Kosmotoga olearia TBF 19.5.1
Mesotoga prima MesG1.Ag.4.2
Streptococcus agalactiae A909 (serotype Ia)
Streptococcus agalactiae 2-22 (serotype Ib)
responsible for several epidemics in fish farms
fish farms in Israel
Israel
Streptococcus agalactiae GD201008-001 (serotype Ia)
farmed tilapia
fish
diseased fish
Helicobacter pylori OK113
Okinawa, Japan
Helicobacter pylori OK310
the Peruvian Amazon
Helicobacter pylori HPAG1
Okinawa Prefectural Chubu Hospital, Uruma, Okinawa, Japan
Okinawa
Ralstonia solanacearum FQY_4
a Bacterial Wilt Nursery Used for Breeding Crop Resistance
a bacterial wilt nursery
a bacterial wilt nursery, which was built for breeding crop resistance
the Guizhou province in southwest China
Xanthomonas citri
Florida
Mexican lime
Palm Beach County in southern Florida
Candidatus Portiera aleyrodidarum TV
whitefly host (Trialeurodes vaporarium)
Candidatus Portiera aleyrodidarum BT-B
the whitefly Bemisia tabaci
Bemisia tabaci
the Bemisia tabaci
Trialeurodes vaporarium colony
Acinetobacter baumannii BJAB0868
Acinetobacter baumannii BJAB0715
Acinetobacter baumannii BJAB07104
ascites
spinal fluid
Beijing, China
cerebrospinal fluid (CSF) sample of a patient with cerebrospinal rhinorrhea
blood sample of a patient with liver cirrhosis
ascites sample of a patient with mesenteric venous thrombosis (MVT)
General Hospital of People’s Liberation Army in Beijing, China
bloodstream
cerebrospinal fluid
clinical samples
Sorangium cellulosum So0157-2
Yunnan Province, China
soil collected from the bank of an alkaline lake (pH 9.0)
alkaline soils near an alkaline lake
Spiroplasma syrphidicola
a syrphid fly (Eristalis arbustorum)
Spiroplasma chrysopicola
a deerfly (Chrysops sp.)
Mesoplasma florum L1
floral surfaces
Alteromonas macleodii AltDE1
seawater sample
the Adriatic Sea
Alteromonas sp. SN2
intertidal sediments
Alteromonas macleodii English Channel 615
the English Channel
the South Adriatic
Alteromonas macleodii Ionian Sea UM7
Urania
Alteromonas macleodii Aegean Sea MED64
the Aegean Sea near Lebanon
Lebanon
Alteromonas macleodii Ionian Sea U4
the Ionian Sea at the Urania Basin (West of Crete)
Alteromonas macleodii Ionian Sea UM4b
Alteromonas macleodii Ionian Sea U8
Alteromonas macleodii Ionian Sea U7
the L4 long-term coastal monitoring station in the Western English Channel
coastal waters
the L4 long-term coastal monitoring station off Plymouth (English Channel)
off Israel (Eastern Aegean)
Methanomassiliicoccus sp. Mx1-Issoire
Human Feces
human gut
Candidatus Methanomethylophilus alvus Mx1201
Sulfolobus islandicus M.16.4
Russia
Sulfolobus islandicus Y.G.57.14
Sulfolobus islandicus REY15A
Sulfolobus islandicus L.S.2.15
Sulfolobus islandicus M.14.25
Sulfolobus islandicus LAL14/1
Sulfolobus islandicus HV10/4
Sulfolobus islandicus L.D.8.5
Sulfolobus islandicus Y.N.15.51
Sulfolobus islandicus M.16.27
a solfataric field
the Mutnovsky Volcano, Kamchatka, Russia
Lassen National Park, USA
Achromobacter xylosoxidans NH44784-1996
a cystic fibrosis patient
the Copenhagen CF Centre
sputum from a cystic fibrosis patient
Streptomyces rapamycinicus
Easter Island
Staphylococcus aureus subsp. aureus CN1 (CA-MRSA)
the Seoul area of South Korea
the pus of a necrotizing fasciitis infection in an 80-year old patient
Acetobacter pasteurianus 386B
a spontaneous cocoa bean heap fermentation
spontaneous cocoa bean fermentations
Burkholderia pseudomallei MSHR305
a fatal encephalomyelitis case
Burkholderia pseudomallei 668
a nonfatal encephalomyelitis case
Burkholderia pseudomallei K96243
the Royal Darwin Hospital, Northern Territory, Australia
an autopsy of a fatal melioidosis encephalomyelitis case
Helicobacter pylori UM032
a patient presenting with peptic ulcer disease
Helicobacter pylori UM299
mouse
Lactococcus lactis subsp. cremoris KW2
fermented corn
kaanga wai (fermented corn)
Lactococcus lactis subsp. cremoris SK11
Lactococcus lactis subsp. cremoris A76
Lactococcus lactis subsp. cremoris UC509.9
Spiroplasma culicicola AES-1
the salt marsh mosquito Aedes sollicitans
Spiroplasma sabaudiense Ar-1343
a mixed pool of Aedes sticticus and Aedes vexans
Spiroplasma diminutum CUAS-1
Culex annulus and Culex tritaeniorhynchus
Spiroplasma taiwanense
mosquitoes
Taiwan
the French Northern Alps
New Jersey, USA
Culex tritaeniorhynchus
Spiroplasma taiwanense CT-1
Mosquito (Aedes)
Culex annulus
Staphylococcus aureus subsp. aureus SA957 (CA-MRSA)
pneumonia patients
patients with severe disease
hospitalized children with various clinical syndromes
Staphylococcus aureus subsp. aureus SA40, community-associated MRSA
healthy children from a surveillance study
Staphylococcus aureus subsp. aureus LGA251
bulk milk that was phenotypically resistant to meticillin but tested negative for the mecA gene
a bulk milk sample
a farm in southwest England
Mycobacterium canettii CIPT 140070017
human tuberculosis patients
Mycobacterium canettii CIPT 140060008
Mycobacterium canettii CIPT 140070010
Mycobacterium canettii CIPT 140070008
Helicobacter pylori BM012S
Helicobacter pylori BM012A
Campylobacter fetus subsp. venerealis cfvi03/293
the lung of an aborted bovine fetus
Bibersteinia trehalosi USDA-ARS-USMARC-190
Cattle with Shipping Fever
Bibersteinia trehalosi USDA-ARS-USMARC-188
Bibersteinia trehalosi USDA-ARS-USMARC-189
Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
a chicken carcass
the skin of a retail chicken
Campylobacter lari RM2100
the Centers for Disease Control and Prevention, Atlanta, Georgia, United States
Deinococcus radiodurans
a contaminant of irradiated canned meat
Neisseria meningitidis MC58 (serogroup B)
a case of invasive infection
Macaubal (São Paulo, Brazil)
Citrus variegated chlorosis-affected Valencia sweet orange twigs
Michigan ground beef
Sakai
Staphylococcus aureus subsp. aureus N315 (MRSA/VSSA)
the pharyngeal smear of a Japanese patient
Staphylococcus aureus subsp. aureus Mu50 (MRSA/VISA)
a patient with wound infection
the pus of a Japanese male baby with a surgical wound infection
a pharyngeal smear
Staphylococcus aureus subsp. aureus MW2 (CA-MRSA)
North Dakota, USA
the pus of a postoperative wound
septic arthritis in a 16-month-old girl
Shewanella oneidensis
sediments
Photorhabdus luminescens
Thermus thermophilus HB27
a natural thermal environment
Brac del Port, Alicante, Spain
salt-saturated crystallizer ponds of a solar saltern
a case of human tularemia
the US
St Bartholomew’s Hospital, London
Pseudomonas protegens Pf-5
the rhizosphere
an upflow anaerobic sludge blanket reactor treating
Beijing, China.
Methanosaeta concilii GP6
Methanosaeta thermophila PT
Staphylococcus aureus subsp. aureus USA300_FPR3757 (CA-MRSA)
the San Francisco General Hospital
a British hospital
the wrist abscess of a 36-year-old HIV-positive white man with a history of injection drug use
Staphylococcus aureus subsp. aureus COL (MRSA)
a mouse model of bacteraemia
Ignicoccus hospitalis
hot rocks and gravel
the Kolbeinsey Ridge, to the north of Iceland
the hydrothermal system
Kolbeinsey Ridge, to the north of Iceland (67° 03′ 46″ N 18° 42′ 64″ E)
a submarine hydrothermal system
Neisseria meningitidis 053442 (serogroup C)
Anhui Province, China
the cerebrospinal fluid of a patient
Anhui Province
North Carolina, USA
Anhui
Patient
Streptococcus suis GZ1
a patient ## ## who had septicemia
Guizhou Province
a patient ## ## ## who had septicemia
biofilm
Dinoroseobacter shibae
single washed cells of the dinoflagellate
Prorocentrum lima
water
Sandy’s Spring West
the United Kingdom
a patient ## ## ## ## with gastritis
Sakai city, Japan
a gastritis patient
a patient with a duodenal ulcer
Salmonella enterica subsp. enterica serovar Typhimurium DT2
Yellowstone, USA
Phaeobacter gallaeciensis DSM 17395
Sulfurimonas denitrificans DSM 1251
Coastal Marine sediment
Salmonella enterica subsp. enterica serovar Typhimurium SL1344
Dinoroseobacter shibae DFL 12
Dinoflagellate culture
Chlamydia trachomatis E/SotonE8
Southampton
streptococcal toxic shock syndrome patient
Kamchatka, Russia
Helicobacter hepaticus
Liver
Chlamydia trachomatis E/SotonE4
Endocervix
Bacillus cereus ZK
Namibia
a swab of a zebra carcass
Michigan
Bacillus thuringiensis 97-27
a necrotic human wound
U. Wisconsin
Salmonella enterica subsp. enterica serovar Typhimurium D23580
Salmonella enterica subsp. enterica serovar Typhimurium DT104
Jannaschia sp. CCS1
California, USA, Bodega Head
Francisella philomiragia subsp. philomiragia ATCC 25017
Utah
Neisseria meningitidis Z2491 (serogroup A)
Streptomyces hygroscopicus subsp. jinggangensis 5008
Lassen, USA
Phaeobacter inhibens DSM 17395
Methanoculleus marisnigri
Pecten maximus, Spanish waters
Chlamydia trachomatis L2b/795
Rectum
Chlamydia trachomatis D/SotonD6
Phaeobacter gallaeciensis 2.10
USA-CA
Ulva lactuca, Australian waters
Grapevine
Neisseria meningitidis alpha14 (cnl strain)
Bavaria, Germany
Peptoclostridium difficile BI1 (Clostridium difficile BI1)
Minneapolis, MN
healthy carriers during a carriage study performed in 1999/2000
Kosmotoga olearia
the North Sea
the Troll B Oil Platform
Bordeaux
Octadecabacter arcticus 238
Offshore Deadhorse, Alaska
Clostridium difficile R20291
Aylesbury, UK
Chlamydia trachomatis D/SotonD5
Clostridium difficile CD196
Paris, France
Geobacillus kaustophilus HTA426
Xylella fastidiosa subsp. sandyi Ann-1
Peptoclostridium difficile 630 (Clostridium difficile 630) (PCR-ribotype 012)
Zurich, Switzerland
Oleander
Chlamydia trachomatis L2b/CV204
Octadecabacter antarcticus 307
McMurdo Sound
surface water
lion
Neisseria meningitidis M01-240149 (serogroup B)
United Kingdom
Citrus
Stoke Mandeville, UK
Paris
Bodega Head, USA
Bartonella bacilliformis KC583
Bartonella grahamii as4aup
Vole
Mouse
Chlamydia trachomatis D/SotonD1
Helicobacter pylori Gambia94/24
a patient with pseudomembranous colitis
Chlamydia trachomatis L2b/LST
Bay of Tokyo
Russian circus
surface of the alga Ulva lactuca
Zurich
United States
Helicobacter hepaticus ATCC 51449
Rodents
surface of macroalga Ulva lactuca
Sulfurovum sp. NBC37-1
Streptococcus pneumoniae INV104
Oxford, UK
Vent sediment
Pacific coastal seawater
Sulfolobus solfataricus P2
Naples, Italy
enrichment cultures obtained from terrestrial acidic hot springs
the Isfjord, Spitsbergen
Propionibacterium freudenreichii
a seawater sample
Bordetella bronchiseptica 253
Cattle
the feral pigeon (Columba livia)
Columba livia (rock or feral pigeon)
Chlamydia trachomatis L3/404/LN
Lymph node
Neisseria meningitidis M01-240355 (serogroup B)
Neumünster, Germany
pigeon
the feral pigeon
U.S.
permanently cold seawater
Sheep
Francisella tularensis subsp. novicida U112
Taylorella equigenitalis MCE9
a stud farm in the Haute-Savoie (France)
Dog
the urethral fossa of a 4-year-old stallion
Colwellia psychrerythraea
Azospirillum brasilense
Neisseria meningitidis alpha14 (contains capsule null locus)
Chlamydia trachomatis E/Bour
Ocular
Arctic marine sediments
Lassen Volcanic National Park
an 80-year-old female enrolled in a Swedish case-control study of gastric adenocarcinoma
Methanosphaera stadtmanae
a patient with chronic atrophic gastritis
the human intestinal environment
French Guyane
Methanobrevibacter smithii ATCC 35061
Methanosphaera stadtmanae DSM 3091
the human gut
Candidatus Methanomethylophilus alvus
the Human Gut
Liberibacter crescens
Ruegeria sp. TM1040
Chesapeake Bay
the peduncle of the tropical Babaco plant
Pfiesteria piscida
Ruegeria pomeroyi DSS-3
Sulfolobus islandicus HVE10/4
Icelandic solfataras
mountain papaya to gain insight on Huanglongbing (HLB) and Zebra Chip (ZC) diseases
India
Legionella longbeachae
mice used in carcinogenesis assays
Coastal Georgia, USA
Opitutus terrae
rice paddy soil
Anus
BR-SP, Macaubal
Artibonite, Haiti
Clostridium acetobutylicum ATCC 824
Connecticut
a carriage study in 8,000 children and young adults in Bavaria, Germany, in 1999/2000
Enteromorpha linza
the Troll B oil platform
oil production fluid
Neisseria meningitidis NZ-05/33 (serogroup B)
Human faeces
Sewage digester
Bovine rumen
Neisseria meningitidis M04-240196 (serogroup B)
Edwardsiella tarda FL6-60
stool
Stoke Mandeville
Penile ulcer
Chlamydia trachomatis L2/434/Bu
a cheese production outfit
a sea-tidal flat
McCoy cells ## ## ## from a urethral sample from a Swedish man, suffering from symptomatic chlamydial urethritis
a crude oil-contaminated sea-tidal flat
Staphylococcus aureus subsp. aureus JH1, meticillin-resistant, vancomycin-susceptible
Escherichia fergusonii
Faeces
Chlamydia trachomatis A/HAR-13
conjunctiva
Streptococcus suis ST3
lymphogranuloma venereum patient
Spiroplasma apis B31
Honeybee
Geobacillus kaustophilus
the Mariana Trench
the deep-sea sediment
Spiroplasma syrphidicola EA-1
Eristalis arbustorum
Syrphid fly
Spiroplasma mirum ATCC 29335 SMCA
Haemaphysalis leporispalustris
Rabbit tick
Spiroplasma chrysopicola DF-1
Chrysops sp.
Deer fly
Mosquito (Culex)
Chlamydia trachomatis L2b/UCH-1/proctitis
a rectal swab of a 49-yr-old men who have sex with men who was HIV positive and Hepatitis C negative
the Lō`ihi Seamount, Hawai
Transkei
the hydrothermal vents
Salmonella enterica subsp. enterica serovar Typhimurium 798
Honeybee (Apis)
the Lōihi submarine volcano, Hawaii
the Lōihi submarine volcano
Staphylococcus aureus subsp. aureus Mu3 (MRSA/hetero-VISA)
a hydrothermal vent
Sulfurimonas denitrificans
coastal marine sediments
Oral
child
Humans
Desulfobacterium autotrophicum
Sydney, Australia
scallop larvae hatchery
Tourcoing
a naturally infected grapevine with Pierce's disease
Burkholderia mallei ATCC 23344
postmortem cultures of knee fluid, skin pustules, and blood of a Chinese soldier who died of a glanders-melioidosis type of infection
Waddlia chondrophila
aborted bovine fetuses
a Minneapolis hospital
near Sydney, Australia
a patient with Clostridium difficile infection
a child with chronic otitis media
the nasopharynx of a child with chronic otitis media
nasopharynx, ## of children with chronic otitis media
a patient with chronic otitis media
Chlamydia trachomatis A/7249
Kahe Mpya, Rombo district
USA (TX)
the Atlantic coast of north western Spain
Chlamydia trachomatis L2b/Canada2
Vancouver
a Paris hospital
Haemophilus influenzae PittGG (nontypeable)
Pittsburgh
a single patient with Clostridium difficile infection
Otorrhea
Dehalococcoides ethenogenes 195
pure culture
Bacteriovorax marinus SJ
hotspring
Haemophilus influenzae PittEE (nontypeable)
otitis media with effusion
coastal sea water
Chlamydia trachomatis L2b/Canada1
Georgia, USA
Bodega Head, CA
Seattle
Chlamydia trachomatis A/5291
Neisseria meningitidis H44/76 (serogroup B)
Blood isolate (meningitis)
Republic of Georgia
Alaska, USA, offshore of Deadhorse
St Louis
otitis media
chronic otitis media patient
Mycoplasma putrefaciens KS1
Antarctica, McMurdo Sound
Antarctica
surface of unidentified seaweed
a marine dinoflagellate culture (Pfiesteria piscicida)
Burkholderia pseudomallei 1106a
Liver pus
Porphyromonas gingivalis TDC60
Atlantic coastal seawater
Japan, Otsuchi Bay
surface of macroalga Ulva linza
Porphyromonas gingivalis W83
Porphyromonas gingivalis ATCC 33277
Chlamydia trachomatis L2b/UCH-2
Japan, Tokyo Bay
larval culture of scallop Pecten maximus
England (United Kingdom)
London
Chlamydia trachomatis L2b/8200/07
Deep sea
Staphylococcus aureus subsp. aureus ED98
Broiler chicken
a chicken with bacterial chondronecrosis with osteomyelitis
Matlab
Chlamydia trachomatis L2/25667R
Rectal biopsy
Neisseria meningitidis G2136 (serogroup B)
Mosquito
Aedes sp.
Streptococcus pneumoniae INV200
Lassen National Park
Burkholderia xenovorans
upper New York State
Ionian Sea, Urania Basin
Trachoma (oculotropic)
a PCB-containing landfill
Chlamydia trachomatis Ia/SotonIa1
Devil’s Kitchen
Black Sea
Staphylococcus aureus subsp. aureus USA300_TCH1516, community-acquired meticillin-susceptible
Cupriavidus taiwanensis
root nodules of Mimosa pudica
Polynucleobacter necessarius subsp. necessarius STIR1
freshwater ciliates
Chlamydia trachomatis G/SotonG1
Chlamydia trachomatis D/UW-3/CX
activated sludge, industrial waste water
Trachoma (genitotropic)
Delftia acidovorans SPH-1
soil, aquatic, sewage
garden soil
Rickettsia felis
Burkholderia xenovorans LB400
rhizosphere, polluted soils, landfills
soil, rhizosphere
Cupriavidus taiwanensis LMG 19424
plant root nodules
the Mutnovksy Volcano in Kamchatka, Russia
Cupriavidus pinatubonensis JMP13 (Ralstonia eutropha JMP134)
soil, aquatic; volcanic mudflow deposits
the Black Sea
heavy metal-rich sediments and soils
Streptococcus pneumoniae SPN994039
Glasgow Reference Lab
Acholeplasma laidlawii
wastewaters
Yamaguchi Central Hospital, Yamaguchi Prefecture, Japan
a patient with septicemia
Bubo
Whiteflies
anoxic sediments
Origin United Kingdom
Chlamydia trachomatis F/SotonF3
Streptococcus pneumoniae SPN994038
Aegean Sea of Lebanon
Streptococcus pneumoniae SPN034183
Streptococcus pneumoniae SPN034156
Chlamydia trachomatis E/C599
Male urethra
Streptococcus pneumoniae OXC141
Chlamydia trachomatis F/SW5
Adriatic Sea
Bovine/bulk milk
Indianapolis, USA
Chlamydia trachomatis F/SW4
Avian
Conjunctiva
Reykjanes, Iceland
Hvergaardi, Iceland
Tick
Malmö, Sweden
Ovine/mastitis
Horse
a clonal population originating from a single plaque-purified isolate
genitotropic
oculotropic
a genitotropic
an oculotropic trachoma
proctitis
bubo
a pig with pneumonia
Saudi Arabia
Urine
Streptococcus suis JS14
Jiangsu Province, China
articulation of a diseased pig
a diseased pig
Streptococcus mutans LJ23
the operating theatre in a hospital in Colindale, England
Streptococcus mutans UA159
the oral cavity of a Japanese patient
adult
a Japanese patient with infection of a surgical incision site
Staphylococcus epidermidis RP62A
intravascular catheter
a 16-month-old girl
the U.S.
Staphylococcus aureus subsp. aureus MSSA476 (MSSA)
a 9-year-old boy with community-acquired primary upper tibial osteomyelitis
Brachyspira pilosicoli P43/6/78
Pig
Wolbachia sp. wRi
southern California
Brachyspira intermedia
a natural Drosophila simulans
Clostridium novyi NT
Gas gangrene
Pear phyllosphere
Staphylococcus aureus subsp. aureus NCTC 8325
the Guangdong province of China
moribund cultural tilapia with meningoencephalitis
Oxfordshire, UK
Sugar beet phyllosphere
meningoencephalitis in cultural tilapia
Tilapia with Meningoencephalitis
Massachusetts, USA
Soil
Mycobacterium bovis BCG Mexico
Texas, USA
N. Ireland (United Kingdom)
Endocarditis Patient (Blood)
Aedes sollicitans
near St John’s Island, US Virgin Islands
Apis mellifera
northern Taiwan
the Iheya North hydrothermal field, Japan
nasopharyngeal swab
in situ samplers deployed on the actively venting sulfide mound
a patient with proctitis
invasive cases
Ciskei
Genital ulcer
Mutnovsky Volcano
Blood
healthy carriers
Kamchatka
clinical lymphogranuloma venereum isolate from a patient with proctitis
Staphylococcus aureus subsp. aureus MRSA252 (MRSA)
a 64-year-old female who acquired MRSA postoperatively
Gauteng
Staphylococcus aureus subsp. aureus JH9 (MRSA/VRSA)
Chlamydia trachomatis L1/440/LN
Staphylococcus epidermidis ATCC 12228
North Dakota
an inguinal bubo of a lymphogranuloma venereum case 40 yr ago
Memphis, Tennessee
Chlamydia trachomatis K/SotonK1
Norris Geyser Valley
lymphogranuloma venereum
Natronomonas pharaonis
Chicken
highly saline soda lakes
Chlamydia trachomatis Ia/SotonIa3
salt-saturated lakes of pH 11
Geyser Creek
Parvibaculum lavamentivorans DS-1
Moreau, New York
PCB-contaminated landfill soil
an alkaline soil sample
Sulfur Works
Poultry
Khon Kaen hospital in Thailand
a 34-year-old female diabetic patient
a case of human melioidosis
English Channel
San Francisco, USA
lymph node
Clostridium acidurici
male urethra
Bovine
cervix
Northern Ireland
Drosophila melano-gaster
Streptococcus suis A7
a human infection
Bulk milk
Somerset, England
Burkholderia thailandensis E264
Chlamydia trachomatis L2c
the rectal mucosa of a male who had a history of sex with men and presented with severe hemorrhagic proctitis
the rectal mucosa of an men who have sex with men
an men who have sex with men with severe hemorrhagic proctitis
Staphylococcus aureus 04-02981
Köln
Helicobacter pylori UM298
Francisella tularensis subsp. holarctica OSU18
near Red Rock, Okla.
a dead beaver
Escherichia coli K-12 MG1655
Live vaccine
trout
Ovine
Oklahoma
Burkholderia pseudomallei 1710b
Listeria monocytogenes EGD-e (serotype 1/2a)
Listeria monocytogenes F2365 (serotype 4b)
a beaver that died of tularemia
Wolinella succinogenes
the rumen of cattle
Wolinella succinogenes DSM 1740
Human & avian
Rodent
Helicobacter acinonychis Sheeba
Helicobacter mustelae
Ferrets
Francisella novicida U112
Water
Burma
Streptococcus suis S735
a case of pneumonia in a pig
the Swine
Ziyang County, Sichuan Province
Xanthomonas campestris pv. vesicatoria
Haian County, Jiangsu Province
Pseudomonas aeruginosa LESB58
a Liverpool cystic fibrosis patient
Temecula, Calif
a naturally infected grapevine
Kazakstan
Streptococcus suis T15
Holland
Wyoming