Strain identifier

BacDive ID: 4428

Type strain: No

Species: Escherichia coli

Strain Designation: W

Strain history: CIP <- 1983, NCIB <- 1954, ATCC <- S.A. Waksman: strain W

NCBI tax ID(s): 566546 (strain), 562 (species)

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General

@ref: 564

BacDive-ID: 4428

DSM-Number: 1116

keywords: genome sequence, Bacteria, mesophilic, motile, antibiotic resistance

description: Escherichia coli W is a mesophilic, motile bacterium that has multiple antibiotic resistances and was isolated from Environment, Soil.

NCBI tax id

NCBI tax idMatching level
566546strain
562species

strain history

@refhistory
564<- ATCC <- S.A. Waksman, strain W
118346CIP <- 1983, NCIB <- 1954, ATCC <- S.A. Waksman: strain W

doi: 10.13145/bacdive4428.20230509.8.1

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: 564

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: W

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.183
6948099.987negative
118346yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
564NUTRIENT 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
41814MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118346CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118346CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
564positivegrowth37mesophilic
41814positivegrowth30mesophilic

Physiology and metabolism

antibiogram

@refmediumPenicillin Goxacillinampicillinticarcillinmezlocillincefalotincefazolincefotaximeaztreonamimipenemtetracyclinechloramphenicolgentamycinamikacinvancomycinerythromycinlincomycinofloxacinnorfloxacincolistinpipemidic acidnitrofurantoinbacitracinpolymyxin bkanamycinneomycindoxycyclineceftriaxoneclindamycinfosfomycinmoxifloxacinlinezolidnystatinquinupristin/dalfopristinteicoplaninpiperacillin/tazobactamincubation temperatureincubation timeoxygen condition
564Mueller-Hinton Agar0018262022283432-34322426242601003434-3612-1426220142220183203430-32000022
564Mueller-Hinton Agar01020262022283432322822-242424120034361626-282401624222032-3403630600020-22371aerob
564Mueller-Hinton Agar00202620-2222-2428363232-3426-28262424-260603236142822-24016222020-2232-3403630-32000020-2237aerob
564Mueller-Hinton Agar001826-2820222834-363432-3424-2624-2624-2624-2608034-3638-4014282201434202036036-3832000022
564Mueller-Hinton Agar00182620202832-343232262422240803436142620-22016242020320343000002237aerob
564Mueller-Hinton Agar00182620202832-343232262422240803436142620-22016242020320343000002237aerob
564Mueller Hinton001824202026-2830303022-242220-222206030-3232-34122620016221818300322800002037aerob

spore formation

@refspore formationconfidence
69481no100
69480no99.767

compound production

@refcompound
564cephalosporins
564diaminopimelate decarboxylase
564glutamine synthetase
564hydrogenase
564penicillin acylase
5646-amino penicillanic acid (amides)
5646 aminopenicillanic acid (amides)

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
6837418257ornithine+degradation
6837429016arginine-hydrolysis
6837425094lysine+degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid+builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol+builds acid from
6837417306maltose+builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan+energy source
6837417634D-glucose+builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose+builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose+builds acid from
6837462345L-rhamnose+builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleyes
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6837435581indole+
6836815688acetoin-
6836835581indole+

enzymes

@refvalueactivityec
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase+3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase+3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase-
68374urease-3.5.1.5
68374lysine decarboxylase+4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase+4.1.1.17
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
564+-++----+--++-++++-+-
564+-++----+--++-++++-+
564+-++----+--++-++++-+-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
44398+-+--+--+-++--+-+-++-+--+++-----

Isolation, sampling and environmental information

isolation

  • @ref: 118346
  • sample type: Environment, Soil
  • country: United States of America
  • origin.country: USA
  • continent: North America

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
5641Risk group (German classification)
1183461Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia coli WGCA_000184185completencbi566546
66792Escherichia coli WGCA_000258145completencbi566546
66792Escherichia coli WGCA_000147755scaffoldncbi566546
66792Escherichia coli W ATCC 9637GCA_008868305contigncbi566546
66792Escherichia coli VKPM B-10182562.5049wgspatric562
66792Escherichia coli W566546.4completepatric566546
66792Escherichia coli W566546.53plasmidpatric566546
66792Escherichia coli W566546.55plasmidpatric566546
66792Escherichia coli W566546.52plasmidpatric566546
66792Escherichia coli W566546.54plasmidpatric566546
66792Escherichia coli W566546.30completepatric566546
66792Escherichia coli W strain ATCC 9637566546.88wgspatric566546
66792Escherichia coli strain W; ATCC 9637562.24207plasmidpatric562
66792Escherichia coli W, ATCC 96372521172717completeimg566546
66792Escherichia coli W, ATCC 9637650377934completeimg566546
66792Escherichia coli W2506520037completeimg566546

GC content

  • @ref: 564
  • GC-content: 51.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.926no
flagellatedno59.274no
gram-positiveno98.294no
anaerobicno94.048no
aerobicyes85.995no
halophileno91.459no
spore-formingno93.964no
thermophileno99.07no
glucose-utilyes93.996no
glucose-fermentyes92.866yes

External links

@ref: 564

culture collection no.: CCUG 1640, DSM 1116, ATCC 9637, CCM 2024, NCIB 8666, NRRL B-766, CIP 2.83, IFO 13500, NCIMB 8666

straininfo link

  • @ref: 73918
  • straininfo: 2806

Reference

@idauthorscataloguedoi/urltitle
564Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1116)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1116
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
41814Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11634
44398Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 1640)https://www.ccug.se/strain?id=1640
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
68374Automatically annotated from API ID32E
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
73918Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2806.1StrainInfo: A central database for resolving microbial strain identifiers
118346Curators of the CIPCollection of Institut Pasteur (CIP 2.83)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%202.83