Strain identifier

BacDive ID: 23925

Type strain: No

Species: Escherichia coli

Strain history: CIP <- 2001, K. Mooijman, Nat. Inst. Public Health and Environ., Bilthoven, The Netherlands: strain WR1

NCBI tax ID(s): 562 (species)

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General

@ref: 20555

BacDive-ID: 23925

DSM-Number: 19683

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

description: Escherichia coli DSM 19683 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
20555<- NCTC; WR1
351692001, K. Mooijman, Nat. Inst. Public Health and Environ., Bilthoven, The Netherlands: strain WR1
118695CIP <- 2001, K. Mooijman, Nat. Inst. Public Health and Environ., Bilthoven, The Netherlands: strain WR1

doi: 10.13145/bacdive23925.20230509.8.1

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: 20555

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

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.163
6948099.99negative
118695negativerod-shaped

colony morphology

  • @ref: 118695

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20555LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
35169MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118695CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20555positivegrowth37mesophilic
35169positivegrowth30mesophilic
118695positivegrowth10-41
118695nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118695
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.821

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin-fermentation
6836828053melibiose+fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11869529864mannitol+fermentation
1186954853esculin-hydrolysis
11869517234glucose+fermentation
11869517716lactose+fermentation
11869517632nitrate+reduction
11869516301nitrite+reduction
11869515792malonate-assimilation
118695132112sodium thiosulfate-builds gas from
11869517234glucose+degradation

antibiotic resistance

  • @ref: 118695
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenyes
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11869535581indoleyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole+
11869515688acetoin-
11869517234glucose+

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
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
118695oxidase-
118695beta-galactosidase+3.2.1.23
118695alcohol dehydrogenase-1.1.1.1
118695gelatinase-
118695catalase+1.11.1.6
118695lysine decarboxylase-4.1.1.18
118695ornithine decarboxylase-4.1.1.17
118695phenylalanine ammonia-lyase-4.3.1.24
118695tryptophan deaminase-
118695urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118695-++--++-+-++-+++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXN2
20555+-------+--++-++-+-+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118695+++++-+--++++++--+-+++-++----+-+-+--+------+++---+----++---+++------++--++-++--+++++--+--++++++-+-+

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typeisolation date
35169NetherlandsNLDEurope
118695NetherlandsNLDEuropeEnvironment, Sewage1978

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
20555yesyes2Risk group (German classification)
1186952Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia coli NCTC13167GCA_900448075contigncbi562
66792Escherichia coli strain NCTC13167562.34134wgspatric562

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.191no
anaerobicno94.742no
halophileno92.173no
spore-formingno94.054no
glucose-utilyes94.005no
thermophileno99.033yes
aerobicyes85.449no
motileyes88.147no
flagellatedno60.137no
glucose-fermentyes92.288yes

External links

@ref: 20555

culture collection no.: DSM 19683, CIP 106878, NCTC 13167, WDCM 00179, WR 1, CCM 7801, CECT 8296

straininfo link

  • @ref: 87926
  • straininfo: 68474

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20555Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-19683Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19683)
35169Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19057
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87926Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID68474.1
118695Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106878Collection of Institut Pasteur (CIP 106878)