Strain identifier
BacDive ID: 159544
Type strain: 
Species: Bifidobacterium tsurumiense
Strain Designation: BSM-380-WT-2B
Strain history: <- D. Wylensek, TU Munich, Freising-Weihenstephan, Germany; BSM-380-WT-2B
NCBI tax ID(s): 356829 (species)
version 9.3 (current version)
General
@ref: 66370
BacDive-ID: 159544
DSM-Number: 104387
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Bifidobacterium tsurumiense BSM-380-WT-2B is a mesophilic bacterium that was isolated from feces; pig, 8 weeks old, wild type.
NCBI tax id
- NCBI tax id: 356829
- Matching level: species
strain history
- @ref: 66370
- history: <- D. Wylensek, TU Munich, Freising-Weihenstephan, Germany; BSM-380-WT-2B
doi: 10.13145/bacdive159544.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Bifidobacteriales
- family: Bifidobacteriaceae
- genus: Bifidobacterium
- species: Bifidobacterium tsurumiense
- full scientific name: Bifidobacterium tsurumiense Okamoto et al. 2008
@ref: 66370
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bifidobacterium
species: Bifidobacterium tsurumiense
full scientific name: Bifidobacterium tsurumiense Okamoto et al. 2008
strain designation: BSM-380-WT-2B
type strain: no
Morphology
cell morphology
- @ref: 125438
- motility: no
- confidence: 95
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 66370 | BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) | yes | https://mediadive.dsmz.de/medium/58 | Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water |
| 66370 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
culture temp
- @ref: 66370
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 92.8
spore formation
- @ref: 125438
- spore formation: no
- confidence: 90.935
Isolation, sampling and environmental information
isolation
- @ref: 66370
- sample type: feces; pig, 8 weeks 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_5384.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_2610;97_3196;98_4013;99_5384&stattab=map
- Last taxonomy: Bifidobacterium tsurumiense subclade
- 16S sequence: MN537465
- Sequence Identity:
- Total samples: 11687
- soil counts: 69
- aquatic counts: 80
- animal counts: 11512
- plant counts: 26
Safety information
risk assessment
- @ref: 66370
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 66370
- description: Bifidobacterium tsurumiense strain DSM 104387 16S ribosomal RNA gene, partial sequence
- accession: MN537465
- length: 1488
- database: nuccore
- NCBI tax ID: 356829
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bifidobacterium tsurumiense BSM-380-WT-2B | GCA_009696505 | contig | ncbi | 356829 |
| 66792 | Bifidobacterium tsurumiense strain BSM-380-WT-2B | 356829.8 | wgs | patric | 356829 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.245 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 77.32 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.935 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 92.496 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 90.989 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 95 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 77.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 75.9 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 65.3 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 92.8 |
External links
@ref: 66370
culture collection no.: DSM 104387
straininfo link
- @ref: 112023
- straininfo: 401735
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 | |
| 66370 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104387 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104387) | |
| 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 | |
| 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/ | |
| 112023 | 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-ID401735.1 | |
| 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 | |
| 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 |