Strain identifier
BacDive ID: 131372
Type strain: 
Species: Bifidobacterium commune
Strain Designation: H23-83
Strain history: <- J. Praet, Univ. Ghent, Belgium; H23-83
NCBI tax ID(s): 1505727 (species)
version 8.1 (current version)
General
@ref: 22599
BacDive-ID: 131372
DSM-Number: 28792
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Bifidobacterium commune H23-83 is an anaerobe, mesophilic bacterium that was isolated from bumblebee gut (Bombus lapidarius.
NCBI tax id
- NCBI tax id: 1505727
- Matching level: species
strain history
- @ref: 22599
- history: <- J. Praet, Univ. Ghent, Belgium; H23-83
doi: 10.13145/bacdive131372.20230509.8.1
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 commune
- full scientific name: Bifidobacterium commune Praet et al. 2015
@ref: 22599
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bifidobacterium
species: Bifidobacterium commune
full scientific name: Bifidobacterium commune Praet et al. 2015
strain designation: H23-83
type strain: yes
Culture and growth conditions
culture medium
- @ref: 22599
- name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)
- growth: yes
- link: https://mediadive.dsmz.de/medium/58
- composition: 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
culture temp
- @ref: 22599
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 22599
- oxygen tolerance: anaerobe
metabolite utilization
| @ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
|---|---|---|---|---|
| 68371 | Potassium 5-ketogluconate | - | builds acid from | |
| 68371 | Potassium 2-ketogluconate | - | builds acid from | |
| 68371 | gluconate | - | builds acid from | 24265 |
| 68371 | L-arabitol | - | builds acid from | 18403 |
| 68371 | D-arabitol | - | builds acid from | 18333 |
| 68371 | L-fucose | - | builds acid from | 18287 |
| 68371 | D-fucose | - | builds acid from | 28847 |
| 68371 | D-tagatose | - | builds acid from | 16443 |
| 68371 | D-lyxose | - | builds acid from | 62318 |
| 68371 | xylitol | - | builds acid from | 17151 |
| 68371 | glycogen | - | builds acid from | 28087 |
| 68371 | starch | - | builds acid from | 28017 |
| 68371 | melezitose | - | builds acid from | 6731 |
| 68371 | inulin | - | builds acid from | 15443 |
| 68371 | trehalose | - | builds acid from | 27082 |
| 68371 | lactose | - | builds acid from | 17716 |
| 68371 | esculin | + | builds acid from | 4853 |
| 68371 | N-acetylglucosamine | - | builds acid from | 59640 |
| 68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
| 68371 | D-sorbitol | - | builds acid from | 17924 |
| 68371 | D-mannitol | - | builds acid from | 16899 |
| 68371 | myo-inositol | - | builds acid from | 17268 |
| 68371 | galactitol | - | builds acid from | 16813 |
| 68371 | L-rhamnose | - | builds acid from | 62345 |
| 68371 | L-sorbose | - | builds acid from | 17266 |
| 68371 | D-mannose | - | builds acid from | 16024 |
| 68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
| 68371 | ribitol | - | builds acid from | 15963 |
| 68371 | L-xylose | - | builds acid from | 65328 |
| 68371 | D-xylose | - | builds acid from | 65327 |
| 68371 | L-arabinose | - | builds acid from | 30849 |
| 68371 | D-arabinose | - | builds acid from | 17108 |
| 68371 | erythritol | - | builds acid from | 17113 |
| 68371 | glycerol | - | builds acid from | 17754 |
API 50CHac
| @ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 22599 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 22599 | - | - | - | - | - | + | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | + | - | + | - | + | + | + | + | - | + | + | - | - | - | + | - | - | - | + | + | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 22599
- sample type: bumblebee gut (Bombus lapidarius
- host species: Bombus lapidarius
- geographic location: Ghent
- country: Belgium
- origin.country: BEL
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Arthropoda | #Insecta |
| #Host Body-Site | #Gastrointestinal tract | #Stomach |
taxonmaps
- @ref: 69479
- File name: preview.99_79841.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_906;97_42613;98_55647;99_79841&stattab=map
- Last taxonomy: Bifidobacterium commune subclade
- 16S sequence: LK054489
- Sequence Identity:
- Total samples: 6341
- soil counts: 79
- aquatic counts: 99
- animal counts: 6112
- plant counts: 51
Safety information
risk assessment
- @ref: 22599
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22599
- description: Bifidobacterium commune partial 16S rRNA gene, type strain LMG 28292T
- accession: LK054489
- length: 1475
- database: ena
- NCBI tax ID: 1505727
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bifidobacterium commune DSM 28792 | GCA_014191315 | contig | ncbi | 1505727 |
| 66792 | Bifidobacterium commune strain DSM 28792 | 1505727.12 | wgs | patric | 1505727 |
| 66792 | Bifidobacterium commune DSM 28792 | 2824199081 | draft | img | 1505727 |
GC content
- @ref: 22599
- GC-content: 54.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 94.551 | no |
| gram-positive | yes | 81.857 | no |
| anaerobic | yes | 96.312 | yes |
| aerobic | no | 97.846 | yes |
| halophile | no | 50 | no |
| spore-forming | no | 97.848 | no |
| thermophile | no | 96.932 | yes |
| glucose-util | yes | 83.853 | no |
| flagellated | no | 95.858 | no |
| glucose-ferment | yes | 78.28 | no |
External links
@ref: 22599
culture collection no.: DSM 28792, LMG 28292
straininfo link
- @ref: 89811
- straininfo: 394198
literature
- topic: Phylogeny
- Pubmed-ID: 25753540
- title: Bifidobacterium commune sp. nov. isolated from the bumble bee gut.
- authors: Praet J, Meeus I, Cnockaert M, Aerts M, Smagghe G, Vandamme P
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-015-0425-3
- year: 2015
- mesh: Animals, Bacterial Typing Techniques, Bees/*microbiology, Bifidobacterium/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Gastrointestinal Tract/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 22599 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28792 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28792) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 68371 | Automatically annotated from API 50CH acid | |||||
| 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/ | |||
| 89811 | 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-ID394198.1 |