Strain identifier
BacDive ID: 158881
Type strain: 
Species: Bacteroides fragilis
Strain Designation: COR2-248-WT-1
Strain history: <- D. Wylensek, TU Munich, Freising-Weihenstephan, Germany <- M. Kornbauer, TU Munich, Freising-Weihenstephan, Germany; COR2-248-WT-1
NCBI tax ID(s): 817 (species)
version 9.3 (current version)
General
@ref: 65703
BacDive-ID: 158881
DSM-Number: 103087
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, human pathogen
description: Bacteroides fragilis COR2-248-WT-1 is a mesophilic, Gram-negative human pathogen that was isolated from feces; pig, 10 month old, wild type.
NCBI tax id
- NCBI tax id: 817
- Matching level: species
strain history
- @ref: 65703
- history: <- D. Wylensek, TU Munich, Freising-Weihenstephan, Germany <- M. Kornbauer, TU Munich, Freising-Weihenstephan, Germany; COR2-248-WT-1
doi: 10.13145/bacdive158881.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Bacteroidaceae
- genus: Bacteroides
- species: Bacteroides fragilis
- full scientific name: Bacteroides fragilis (Veillon and Zuber 1898) Castellani and Chalmers 1919 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Bacillus fragilis
@ref: 65703
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Bacteroides
species: Bacteroides fragilis
full scientific name: Bacteroides fragilis (Veillon and Zuber 1898) Castellani and Chalmers 1919 emend. Hahnke et al. 2016
strain designation: COR2-248-WT-1
type strain: no
Morphology
cell morphology
- @ref: 125438
- gram stain: negative
- confidence: 91.404
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 65703 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
| 65703 | FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) | yes | https://mediadive.dsmz.de/medium/1203 | Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water |
| 65703 | WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) | yes | https://mediadive.dsmz.de/medium/339 | Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water |
culture temp
- @ref: 65703
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68380 | 27897 | tryptophan | - | energy source |
| 68380 | 29985 | L-glutamate | + | degradation |
| 68380 | 16634 | raffinose | + | fermentation |
| 68380 | 16024 | D-mannose | + | fermentation |
| 68380 | 29016 | arginine | - | hydrolysis |
| 68380 | 16199 | urea | - | hydrolysis |
| 68380 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68380 | serine arylamidase | - | |
| 68380 | histidine arylamidase | - | |
| 68380 | glutamyl-glutamate arylamidase | + | |
| 68380 | glycin arylamidase | - | |
| 68380 | tyrosine arylamidase | - | |
| 68380 | leucine arylamidase | + | 3.4.11.1 |
| 68380 | proline-arylamidase | - | 3.4.11.5 |
| 68380 | L-arginine arylamidase | + | |
| 68380 | alkaline phosphatase | + | 3.1.3.1 |
| 68380 | alpha-fucosidase | + | 3.2.1.51 |
| 68380 | glutamate decarboxylase | + | 4.1.1.15 |
| 68380 | beta-glucuronidase | - | 3.2.1.31 |
| 68380 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
| 68380 | alpha-arabinosidase | - | 3.2.1.55 |
| 68380 | beta-glucosidase | + | 3.2.1.21 |
| 68380 | alpha-glucosidase | + | 3.2.1.20 |
| 68380 | beta-Galactosidase 6-phosphate | - | |
| 68380 | alpha-galactosidase | + | 3.2.1.22 |
| 68380 | arginine dihydrolase | - | 3.5.3.6 |
| 68380 | urease | - | 3.5.1.5 |
| 68380 | alanine arylamidase | + | 3.4.11.2 |
| 68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
| 68380 | phenylalanine arylamidase | - | |
| 68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
| 68380 | tryptophan deaminase | - | 4.1.99.1 |
| 68380 | beta-galactosidase | + | 3.2.1.23 |
API rID32A
| @ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 65703 | - | - | + | + | - | + | + | - | - | + | + | + | + | + | - | - | + | + | - | + | - | + | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
- @ref: 65703
- sample type: feces; pig, 10 month old, wild type
- geographic location: Kranzberg (Bavaria)
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
| #Host | #Mammals | #Suidae (Pig,Swine) |
taxonmaps
- @ref: 69479
- File name: preview.99_40.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_34;97_35;98_38;99_40&stattab=map
- Last taxonomy: Bacteroides fragilis subclade
- 16S sequence: MN537460
- Sequence Identity:
- Total samples: 221995
- soil counts: 2825
- aquatic counts: 7159
- animal counts: 211201
- plant counts: 810
Safety information
risk assessment
- @ref: 65703
- pathogenicity human: yes
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 65703
- description: Bacteroides fragilis strain DSM 103087 16S ribosomal RNA gene, partial sequence
- accession: MN537460
- length: 1479
- database: nuccore
- NCBI tax ID: 817
Genome sequences
- @ref: 66792
- description: Bacteroides fragilis COR2-248-WT-1
- accession: GCA_012844105
- assembly level: contig
- database: ncbi
- NCBI tax ID: 817
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 91.404 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 77.863 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 85.948 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.438 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.494 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 87.5 | no |
External links
@ref: 65703
culture collection no.: DSM 103087
straininfo link
- @ref: 111400
- straininfo: 397996
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 | |
| 65703 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103087 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103087) | |
| 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 | |
| 68380 | Automatically annotated from API rID32A | |||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 111400 | 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-ID397996.1 | |
| 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 |