Strain identifier
BacDive ID: 169234
Type strain: 
Species: Escherichia coli
Strain Designation: Ec3550
Strain history: <- T. Clavel, RWTH Aachen; <- B. Stecher, Max von Pettenkofer-Inst., Munich; Ec3550
NCBI tax ID(s): 562 (species)
version 9.3 (current version)
General
@ref: 68478
BacDive-ID: 169234
DSM-Number: 112118
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, human pathogen
description: Escherichia coli Ec3550 is a mesophilic, Gram-negative human pathogen that was isolated from gut content; S. Tm infected, SPF, C57BL/6 mouse.
NCBI tax id
- NCBI tax id: 562
- Matching level: species
strain history
- @ref: 68478
- history: <- T. Clavel, RWTH Aachen; <- B. Stecher, Max von Pettenkofer-Inst., Munich; Ec3550
doi: 10.13145/bacdive169234.20250331.9.3
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: 68478
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacterales
family: Enterobacteriaceae
genus: Escherichia
species: Escherichia coli
full scientific name: Escherichia coli (Migula 1895) Castellani and Chalmers 1919
strain designation: Ec3550
type strain: no
Morphology
cell morphology
- @ref: 125438
- gram stain: negative
- confidence: 99.75
Culture and growth conditions
culture medium
- @ref: 68478
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
culture temp
- @ref: 68478
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
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 | ornithine decarboxylase | + | 4.1.1.17 |
| 68368 | lysine decarboxylase | + | 4.1.1.18 |
| 68368 | cytochrome oxidase | - | 1.9.3.1 |
| 68368 | gelatinase | - | |
| 68368 | tryptophan deaminase | - | 4.1.99.1 |
| 68368 | urease | - | 3.5.1.5 |
| 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 | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 68478 | + | - | + | + | - | - | - | - | + | - | - | + | + | - | + | + | - | + | - | + | - |
Isolation, sampling and environmental information
isolation
- @ref: 68478
- sample type: gut content; S. Tm infected, SPF, C57BL/6 mouse
- geographic location: Munich
- country: Germany
- origin.country: DEU
- continent: Europe
Safety information
risk assessment
- @ref: 68478
- pathogenicity human: yes
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 124043
- description: Escherichia coli strain DSM 112118 16S ribosomal RNA gene, partial sequence.
- accession: OM658578
- length: 1477
- database: nuccore
- NCBI tax ID: 562
Genome sequences
- @ref: 66792
- description: Escherichia coli EC_550
- accession: GCA_015160735
- assembly level: scaffold
- database: ncbi
- 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 | 95.79 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 56.561 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.948 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.5 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 75.706 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 79.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 55.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 70.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 89.2 |
External links
@ref: 68478
culture collection no.: DSM 112118
straininfo link
- @ref: 115476
- straininfo: 401002
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 68368 | Automatically annotated from API 20E | |||
| 68478 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-112118 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 112118) | |
| 115476 | Reimer, 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 identifiers | 10.60712/SI-ID401002.1 | |
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | ||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |