Strain identifier

BacDive ID: 4737

Type strain: No

Species: Escherichia coli

Strain Designation: Bacdive 4737, Stoke W

Strain history: CIP <- 1952, L. Le Minor, Inst. Pasteur, Paris, France <- F. Kauffmann, Stat. Ser., Copenhagen, Denmark: strain Stoke W

NCBI tax ID(s): 562 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3857

BacDive-ID: 4737

DSM-Number: 10234

keywords: genome sequence, Bacteria, facultative anaerobe, mesophilic, motile, human pathogen

description: Escherichia coli Bacdive 4737 is a facultative anaerobe, mesophilic, motile human pathogen of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 562
  • Matching level: species

strain history

@refhistory
3857<- NCIMB <- NCTC <- F. Kauffmann
118347CIP <- 1952, L. Le Minor, Inst. Pasteur, Paris, France <- F. Kauffmann, Stat. Ser., Copenhagen, Denmark: strain Stoke W

doi: 10.13145/bacdive4737.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Escherichia
  • species: Escherichia coli
  • full scientific name: Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Bacillus coli

@ref: 3857

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Escherichia

species: Escherichia coli

full scientific name: Escherichia coli (Migula 1895) Castellani and Chalmers 1919

strain designation: Bacdive 4737, Stoke W

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.056
6948099.976negative
118347nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3857NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33547MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118347CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3857positivegrowth37mesophilic
33547positivegrowth30mesophilic
118347positivegrowth30-41
118347nogrowth5psychrophilic
118347nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118347
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.625

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368L-arabinose+fermentation30849
68368amygdalin-fermentation27613
68368melibiose+fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol+fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan+energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine+degradation18257
68368lysine+degradation25094
68368arginine-hydrolysis29016
118347mannitol+fermentation29864
118347citrate-carbon source16947
118347glucose+fermentation17234
118347lactose+fermentation17716
118347nitrate+reduction17632
118347nitrite+reduction16301
118347malonate-assimilation15792
118347sodium thiosulfate-builds gas from132112
118347glucose+degradation17234

antibiotic resistance

  • @ref: 118347
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11834735581indoleyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole+
11834715688acetoin-
11834717234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
118347oxidase-
118347beta-galactosidase+3.2.1.23
118347alcohol dehydrogenase-1.1.1.1
118347gelatinase-
118347catalase+1.11.1.6
118347lysine decarboxylase+4.1.1.18
118347ornithine decarboxylase+4.1.1.17
118347phenylalanine ammonia-lyase-4.3.1.24
118347tryptophan deaminase-
118347urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118347-+++-++-+-++-+++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
3857+-++----+--++-+--+-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118347+-+/-+++---++++-++/--++--+-+/-+/-+/--+++++--+--------+--+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118347+++++-+++++++++--+++++-++----+-+-+----+----++--+++---+++--+++--------------+---++-+------++++++-+--

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typegeographic location
33547United KingdomGBREurope
45530United KingdomGBREuropeInfantile gastroenteritisScotland
118347United KingdomGBREuropeHuman, Child, feces

isolation source categories

Cat1Cat2
#Infection#Disease
#Host Body-Site#Gastrointestinal tract
#Host#Juvenile

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
3857yesyes2Risk group (German classification)
1183472Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia coli NCTC9111GCA_900449905contigncbi562
66792Escherichia coli strain NCTC9111562.34293wgspatric562

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.216no
anaerobicno95.314no
halophileno89.815no
spore-formingno94.063no
glucose-utilyes94.246no
thermophileno98.838yes
flagellatedno56.37no
motileyes88.025no
aerobicyes89.029no
glucose-fermentyes92.826no

External links

@ref: 3857

culture collection no.: DSM 10234, NCIMB 13058, NCTC 9111, CCUG 11412, ATCC 33780, CIP 52.167

straininfo link

  • @ref: 74235
  • straininfo: 40684

Reference

@idauthorscataloguedoi/urltitle
3857Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10234)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10234
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
33547Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14400
45530Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 11412)https://www.ccug.se/strain?id=11412
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74235Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40684.1StrainInfo: A central database for resolving microbial strain identifiers
118347Curators of the CIPCollection of Institut Pasteur (CIP 52.167)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2052.167