Strain identifier

BacDive ID: 4896

Type strain: No

Species: Escherichia coli

Strain Designation: C2

Strain history: <- J.-L. Garcia

NCBI tax ID(s): 562 (species)

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General

@ref: 5240

BacDive-ID: 4896

DSM-Number: 14166

keywords: genome sequence, Bacteria, mesophilic, human pathogen

description: Escherichia coli C2 is a mesophilic human pathogen that was isolated from Anaerobic digester fed with shea cake, previously inoculated with anaerobic sludge from pit of a slaughter house.

NCBI tax id

  • NCBI tax id: 562
  • Matching level: species

strain history

  • @ref: 5240
  • history: <- J.-L. Garcia

doi: 10.13145/bacdive4896.20230509.8.1

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: 5240

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: C2

type strain: no

Culture and growth conditions

culture medium

  • @ref: 5240
  • name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/381
  • composition: Name: 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

culture temp

  • @ref: 5240
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

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
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
5240+-++----+--++-++++-+-

Isolation, sampling and environmental information

isolation

  • @ref: 5240
  • sample type: Anaerobic digester fed with shea cake, previously inoculated with anaerobic sludge from pit of a slaughter house
  • country: Burkina Faso
  • origin.country: BFA
  • continent: Africa

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Anaerobic digestor
#Engineered#Food production#Meat
#Engineered#Industrial
#Condition#Anoxic (anaerobic)

Safety information

risk assessment

  • @ref: 5240
  • 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 C2GCA_001900495completencbi562
66792Escherichia coli C2GCA_010820545contigncbi562
66792Escherichia coli C2GCA_014892375contigncbi562
66792Escherichia coli C22718218309completeimg562
66792Escherichia coli C2GCA_024518935contigncbi562

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno61.527no
gram-positiveno98.294no
anaerobicno94.803no
aerobicyes86.569no
halophileno90.079no
spore-formingno93.791no
thermophileno99.008no
glucose-utilyes94.771no
motileyes88.609no
glucose-fermentyes92.85no

External links

@ref: 5240

culture collection no.: DSM 14166

straininfo link

  • @ref: 74394
  • straininfo: 49550

Reference

@idauthorscataloguedoi/urltitle
5240Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14166)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14166
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
74394Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49550.1StrainInfo: A central database for resolving microbial strain identifiers