Strain identifier
BacDive ID: 4671
Type strain: 
Species: Escherichia coli
Strain history: <- ATCC <- R.C. Clowes <- Microb. Genet. Research Unit, London
NCBI tax ID(s): 562 (species)
version 9.3 (current version)
General
@ref: 3318
BacDive-ID: 4671
DSM-Number: 8589
keywords: genome sequence, Bacteria, mesophilic, Gram-negative
description: Escherichia coli DSM 8589 is a mesophilic, Gram-negative bacterium of the family Enterobacteriaceae.
NCBI tax id
- NCBI tax id: 562
- Matching level: species
strain history
- @ref: 3318
- history: <- ATCC <- R.C. Clowes <- Microb. Genet. Research Unit, London
doi: 10.13145/bacdive4671.20250331.9.3
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: 3318
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
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 93.6 |
| 125438 | negative | 99.75 |
Culture and growth conditions
culture medium
- @ref: 3318
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
- @ref: 3318
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: aerobe
- confidence: 91.3
spore formation
- @ref: 125439
- spore formation: no
- confidence: 93.8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68368 | 30849 | L-arabinose | + | fermentation |
| 68368 | 27613 | amygdalin | - | fermentation |
| 68368 | 28053 | melibiose | + | fermentation |
| 68368 | 17992 | sucrose | - | fermentation |
| 68368 | 62345 | L-rhamnose | + | fermentation |
| 68368 | 30911 | sorbitol | + | fermentation |
| 68368 | 17268 | myo-inositol | - | fermentation |
| 68368 | 16899 | D-mannitol | + | fermentation |
| 68368 | 17634 | D-glucose | + | fermentation |
| 68368 | 5291 | gelatin | - | hydrolysis |
| 68368 | 27897 | tryptophan | + | energy source |
| 68368 | 16199 | urea | - | hydrolysis |
| 68368 | 16947 | citrate | - | assimilation |
| 68368 | 18257 | ornithine | - | degradation |
| 68368 | 25094 | lysine | + | degradation |
| 68368 | 29016 | arginine | - | hydrolysis |
metabolite production
| @ref | Chebi-ID | metabolite | production |
|---|---|---|---|
| 68368 | 15688 | acetoin | no |
| 68368 | 35581 | indole | yes |
| 68368 | 16136 | hydrogen sulfide | no |
metabolite tests
| @ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
|---|---|---|---|---|
| 68368 | 15688 | acetoin | - | |
| 68368 | 35581 | indole | + |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68368 | gelatinase | - | |
| 68368 | urease | - | 3.5.1.5 |
| 68368 | tryptophan deaminase | - | 4.1.99.1 |
| 68368 | ornithine decarboxylase | - | 4.1.1.17 |
| 68368 | lysine decarboxylase | + | 4.1.1.18 |
| 68368 | arginine dihydrolase | - | 3.5.3.6 |
| 68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
| @ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3318 | + | - | + | - | - | - | - | - | + | - | - | + | + | - | + | + | - | + | - | + |
Safety information
risk assessment
- @ref: 3318
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Escherichia coli ATCC 23740 | GCA_019550865 | contig | ncbi | 562 |
| 66792 | Escherichia coli strain ATCC 23740 | 562.78131 | wgs | patric | 562 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.75 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.783 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.948 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 59.698 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.25 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 75.356 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 93.8 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 61.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 93.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 91.3 |
External links
@ref: 3318
culture collection no.: DSM 8589, ATCC 23740
straininfo link
- @ref: 74166
- straininfo: 38212
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 3318 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8589) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8589 | |
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 68368 | Automatically annotated from API 20E | |||
| 74166 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38212.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |