Strain identifier

BacDive ID: 4410

Type strain: No

Species: Escherichia coli

Strain Designation: B3, B subscript 3 (thy -)

Strain history: <- Institut für Mikrobiologie, Universität Göttingen (IMG), Germany; IMG 1728 <- Lezius; B subscript 3 (thy -) <- A. D. Larson, Karolinska Inst., Stockholm, Sweden;

NCBI tax ID(s): 562 (species)

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General

@ref: 37

BacDive-ID: 4410

DSM-Number: 308

keywords: genome sequence, Bacteria, mesophilic, human pathogen

description: Escherichia coli B3 is a mesophilic human pathogen of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 562
  • Matching level: species

strain history

  • @ref: 37
  • history: <- Institut für Mikrobiologie, Universität Göttingen (IMG), Germany; IMG 1728 <- Lezius; B subscript 3 (thy -) <- A. D. Larson, Karolinska Inst., Stockholm, Sweden;

doi: 10.13145/bacdive4410.20250331.9.3

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: 37

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: B3, B subscript 3 (thy -)

type strain: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
37NUTRIENT 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
37COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf

culture temp

  • @ref: 37
  • growth: positive
  • type: growth
  • temperature: 37

Physiology and metabolism

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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole+

enzymes

@refvalueactivityec
68368gelatinase-
68368urease-3.5.1.5
68368cytochrome oxidase-1.9.3.1
68368tryptophan deaminase-4.1.99.1
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
37+-+-----+--++--+-+-+-
37+-+-----+--++--+-+-+

Safety information

risk assessment

  • @ref: 37
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia coli B3GCA_001561135contigncbi562
66792Escherichia coli B32740892020draftimg562

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidence
125439BacteriaNetspore_formationAbility to form endo- or exosporesno86.6
125439BacteriaNetmotilityAbility to perform movementyes56.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative72.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe79.8

External links

@ref: 37

culture collection no.: DSM 308, IMG 1728

straininfo link

  • @ref: 73900
  • straininfo: 47139

Reference

@idauthorscataloguedoi/urltitle
37Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 308)https://www.dsmz.de/collection/catalogue/details/culture/DSM-308
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
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
73900Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47139.1StrainInfo: A central database for resolving microbial strain identifiers
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1