Strain identifier
BacDive ID: 1750
Type strain:
Species: Bifidobacterium bohemicum
Strain Designation: JEMLUCVIII-4
Strain history: CCM 7729 <-- J. Killer JEMLUCVIII-4.
NCBI tax ID(s): 1437606 (strain), 638617 (species)
General
@ref: 16506
BacDive-ID: 1750
DSM-Number: 22767
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Bifidobacterium bohemicum JEMLUCVIII-4 is an anaerobe, mesophilic bacterium that was isolated from bumblebee digestive tract.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1437606 | strain |
638617 | species |
strain history
@ref | history |
---|---|
16506 | <- J. Killer, Inst. Animal Physiology and Genetics, Academy Sci. of the Czech Republic, Prague; JEMLUCVIII-4 |
67770 | CCM 7729 <-- J. Killer JEMLUCVIII-4. |
doi: 10.13145/bacdive1750.20230509.8.1
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 bohemicum
- full scientific name: Bifidobacterium bohemicum Killer et al. 2011
@ref: 16506
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bifidobacterium
species: Bifidobacterium bohemicum
full scientific name: Bifidobacterium bohemicum Killer et al. 2011 emend. Nouioui et al. 2018
strain designation: JEMLUCVIII-4
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 90.874 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 16506
- 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 | growth | type | temperature | range |
---|---|---|---|---|
16506 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
16506 | anaerobe | |
69480 | anaerobe | 99.503 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
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 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | + | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | + | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | + | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | + | builds acid from | 18305 |
68371 | amygdalin | + | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | + | builds acid from | 320061 |
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 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
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 | D-ribose | + | builds acid from | 16988 |
68371 | L-arabinose | + | builds acid from | 30849 |
68371 | erythritol | - | builds acid from | 17113 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16506 | - | +/- | - | +/- | + | + | + | - | - | + | + | + | + | + | + | - | - | - | - | - | - | + | + | + | + | + | + | - | - | - | + | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
16506 | bumblebee (Bombus lucorum) digestive tract | Bombus lucorum | South Bohemian Region | Czech Republic | CZE | Europe |
67770 | Digestive tract contents of a bumblebee (Bombus lucorum) from South Bohemia | Bombus lucorum | Czech Republic | CZE | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Arthropoda | #Insecta |
#Host Body-Site | #Gastrointestinal tract |
taxonmaps
- @ref: 69479
- File name: preview.99_1596.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_906;97_1056;98_1261;99_1596&stattab=map
- Last taxonomy: Bifidobacterium bohemicum subclade
- 16S sequence: LC521981
- Sequence Identity:
- Total samples: 4171
- soil counts: 102
- aquatic counts: 62
- animal counts: 3988
- plant counts: 19
Safety information
risk assessment
- @ref: 16506
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
16506 | Bifidobacterium bohemicum DSM 22767 16S ribosomal RNA gene, partial sequence | FJ858736 | 1228 | ena | 1437606 |
67770 | Bifidobacterium bohemicum JCM 18049 gene for 16S rRNA, partial sequence | LC521981 | 1461 | ena | 638617 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bifidobacterium bohemicum DSM 22767 | 1437606.5 | wgs | patric | 1437606 |
66792 | Bifidobacterium bohemicum DSM 22767 | 1437606.3 | wgs | patric | 1437606 |
66792 | Bifidobacterium bohemicum DSM 22767 | 2657244953 | draft | img | 1437606 |
66792 | Bifidobacterium bohemicum DSM 22767 | 2597490239 | draft | img | 1437606 |
67770 | Bifidobacterium bohemicum DSM 22767 | GCA_000771605 | contig | ncbi | 1437606 |
67770 | Bifidobacterium bohemicum DSM 22767 | GCA_000741525 | contig | ncbi | 1437606 |
GC content
- @ref: 16506
- GC-content: 51.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 94.2 | no |
gram-positive | yes | 94.533 | no |
anaerobic | yes | 93.287 | no |
halophile | no | 52.383 | no |
spore-forming | no | 95.39 | no |
glucose-util | yes | 87.196 | no |
aerobic | no | 97.575 | yes |
flagellated | no | 96.866 | no |
glucose-ferment | yes | 84.106 | no |
thermophile | no | 93.62 | yes |
External links
@ref: 16506
culture collection no.: DSM 22767, CCM 7729, JCM 18049, KCTC 15184
straininfo link
- @ref: 71397
- straininfo: 377596
literature
- topic: Phylogeny
- Pubmed-ID: 20656822
- title: Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract.
- authors: Killer J, Kopecny J, Mrazek J, Koppova I, Havlik J, Benada O, Kott T
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.022525-0
- year: 2010
- mesh: Aldehyde-Lyases/metabolism, Animals, Bees/*microbiology, Bifidobacterium/*classification/genetics/*isolation & purification, Chaperonin 60/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gastrointestinal Tract/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16506 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22767) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22767 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
71397 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID377596.1 | StrainInfo: A central database for resolving microbial strain identifiers |