Strain identifier
BacDive ID: 4929
Type strain: 
Species: Escherichia sp.
Strain Designation: 3/2/53, 3_2_53FAA
Strain history: <- E. Allen-Vercoe, Univ. Guelph, Ontario, Canada; 3/2/53
NCBI tax ID(s): 1884818 (species)
version 9.3 (current version)
General
@ref: 17781
BacDive-ID: 4929
DSM-Number: 24827
keywords: genome sequence, Bacteria, mesophilic, Gram-negative
description: Escherichia sp. 3/2/53 is a mesophilic, Gram-negative bacterium that was isolated from human gut biopsy.
NCBI tax id
- NCBI tax id: 1884818
- Matching level: species
strain history
- @ref: 17781
- history: <- E. Allen-Vercoe, Univ. Guelph, Ontario, Canada; 3/2/53
doi: 10.13145/bacdive4929.20250331.9.3
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 sp.
- full scientific name: Escherichia Castellani and Chalmers 1919 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Atlantibacter
@ref: 17781
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Enterobacteriaceae
genus: Escherichia
species: Escherichia sp.
full scientific name: Escherichia sp.
strain designation: 3/2/53, 3_2_53FAA
type strain: no
Morphology
cell morphology
- @ref: 125438
- gram stain: negative
- confidence: 99.75
Culture and growth conditions
culture medium
| @ref | name | growth | link |
|---|---|---|---|
| 17781 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf |
| 17781 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf |
culture temp
- @ref: 17781
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 96.1
Isolation, sampling and environmental information
isolation
- @ref: 17781
- sample type: human gut biopsy
- geographic location: Alberta, Calgary
- country: Canada
- origin.country: CAN
- continent: North America
- latitude: 51.0486
- longitude: -114.071
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Patient | #Biopsy |
| #Host | #Human | |
| #Host Body-Site | #Gastrointestinal tract | #Stomach |
Sequence information
Genome sequences
- @ref: 66792
- description: Escherichia sp. 3_2_53FAA
- accession: 469598.5
- assembly level: wgs
- database: patric
- NCBI tax ID: 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 | 96.052 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.198 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 67.65 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.5 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 76.975 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 96.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 50.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 82.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 85.8 |
External links
@ref: 17781
culture collection no.: DSM 24827, BEI HM-38
straininfo link
- @ref: 74426
- straininfo: 404354
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 17781 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24827) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24827 | |
| 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) | |
| 74426 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404354.1 | 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 |