Strain identifier

BacDive ID: 131714

Type strain: No

Species: Escherichia coli

Strain Designation: 83972

Strain history: <- U. Dobrindt, Univ. Münster, Germany; 83972 <- U. Lindberg, Dept. of Paediatrics and Department of Immunology, Institute of Medical Microbiology, University of Gothenburg

NCBI tax ID(s): 562 (species)

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General

@ref: 23510

BacDive-ID: 131714

DSM-Number: 103539

keywords: genome sequence, Bacteria, Gram-negative, human pathogen

description: Escherichia coli 83972 is a Gram-negative human pathogen that was isolated from Urine of Swedish school girl.

NCBI tax id

  • NCBI tax id: 562
  • Matching level: species

strain history

  • @ref: 23510
  • history: <- U. Dobrindt, Univ. Münster, Germany; 83972 <- U. Lindberg, Dept. of Paediatrics and Department of Immunology, Institute of Medical Microbiology, University of Gothenburg

doi: 10.13145/bacdive131714.20240916.9.1

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: 23510

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: 83972

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.75

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23510LB (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
23510TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

  • @ref: 23510
  • growth: positive
  • type: growth
  • temperature: 37

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate+reduction
6836830849L-arabinose+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

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteyes
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

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
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SUREGELGLUMANINOSorRHASACMELAMYARATDA TrpINDVPOXNO2N2
23510++++----++-++-+++
23510++++----++-++-+-+-++
23510+-++----++-++-+-+-++/--+-

Isolation, sampling and environmental information

isolation

  • @ref: 23510
  • sample type: Urine of Swedish school girl
  • geographic location: Gothenborg
  • country: Sweden
  • origin.country: SWE
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host#Human#Female
#Host Body Product#Fluids#Urine

Safety information

risk assessment

  • @ref: 23510
  • 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 83972GCA_000159295scaffoldncbi525281
66792Escherichia coli 83972525281.3wgspatric525281
66792Escherichia coli 83972643886067draftimg525281
66792Escherichia coli 83972GCA_021559815completencbi562

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.75no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.123no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no68.053no
69480spore-formingspore-formingAbility to form endo- or exosporesno88.948no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.5no
69480flagellatedmotile2+Ability to perform flagellated movementyes78.816no

External links

@ref: 23510

culture collection no.: DSM 103539

straininfo link

  • @ref: 90105
  • straininfo: 401296

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
23510Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103539Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103539)
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
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
90105Reimer, 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-ID401296.1