Strain identifier
BacDive ID: 1694
Type strain:
Species: Bifidobacterium boum
Strain Designation: RU917
Strain history: ATCC 27917 <-- V. Scardovi RU 917.
NCBI tax ID(s): 1410645 (strain), 78343 (species)
General
@ref: 8808
BacDive-ID: 1694
DSM-Number: 20432
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive
description: Bifidobacterium boum RU917 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from bovine rumen.
NCBI tax id
NCBI tax id | Matching level |
---|---|
78343 | species |
1410645 | strain |
strain history
@ref | history |
---|---|
8808 | <- ATCC <- V. Scardovi, RU917 |
67770 | ATCC 27917 <-- V. Scardovi RU 917. |
doi: 10.13145/bacdive1694.20230509.8.1
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 boum
- full scientific name: Bifidobacterium boum Scardovi et al. 1979 (Approved Lists 1980)
@ref: 8808
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bifidobacterium
species: Bifidobacterium boum
full scientific name: Bifidobacterium boum Scardovi et al. 1979
strain designation: RU917
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 8808
- 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 |
---|---|---|---|---|
8808 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
8808 | anaerobe | |
69480 | anaerobe | 99.446 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 98 |
69480 | no | 99.999 |
murein
- @ref: 8808
- murein short key: A11.38
- type: A4alpha L-Lys-D-Ser-D-Glu
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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8808 | - | - | - | - | - | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | + | - | - | - | + | - | - | + | - | + | + | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
8808 | bovine rumen |
67770 | Rumen of cattle |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Bovinae (Cow, Cattle) |
#Host Body-Site | #Organ | #Rumen |
taxonmaps
- @ref: 69479
- File name: preview.99_4818.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_607;97_710;98_3608;99_4818&stattab=map
- Last taxonomy: Bifidobacterium boum subclade
- 16S sequence: LC071799
- Sequence Identity:
- Total samples: 18715
- soil counts: 313
- aquatic counts: 200
- animal counts: 18077
- plant counts: 125
Safety information
risk assessment
- @ref: 8808
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bifidobacterium boum strain DSM 20432 16S ribosomal RNA gene, partial sequence | GQ487635 | 141 | ena | 78343 |
20218 | Bifidobacterium boum culture-collection DSM:20432 16S-23S ribosomal RNA intergenic spacer, partial sequence | JQ363654 | 421 | ena | 78343 |
20218 | Bifidobacterium boum gene for 16S rRNA, partial sequence, strain: JCM 1211 | AB116287 | 479 | ena | 78343 |
20218 | Bifidobacterium boum gene for 16S rRNA, partial sequence, strain: JCM 1211 | AB507082 | 669 | ena | 78343 |
20218 | Bifidobacterium boum gene for 16S rRNA, partial sequence, strain: JCM 1211 | D86190 | 1517 | ena | 78343 |
20218 | Bifidobacterium boum strain KCTC 3227 16S ribosomal RNA gene, partial sequence | GU361814 | 1481 | ena | 78343 |
67770 | Bifidobacterium boum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1211 | LC071799 | 1421 | ena | 78343 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bifidobacterium boum DSM 20432 | 1410645.4 | wgs | patric | 1410645 |
66792 | Bifidobacterium boum DSM 20432 | 1410645.3 | wgs | patric | 1410645 |
66792 | Bifidobacterium boum strain LMG 10736 | 78343.3 | wgs | patric | 78343 |
66792 | Bifidobacterium boum LMG 10736 | 2600254979 | draft | img | 78343 |
66792 | Bifidobacterium boum DSM 20432 | 2681813198 | draft | img | 1410645 |
66792 | Bifidobacterium boum DSM 20432 | 2558860116 | draft | img | 1410645 |
67770 | Bifidobacterium boum DSM 20432 | GCA_000771385 | contig | ncbi | 1410645 |
67770 | Bifidobacterium boum LMG 10736 | GCA_000741535 | contig | ncbi | 78343 |
67770 | Bifidobacterium boum DSM 20432 | GCA_000687615 | scaffold | ncbi | 1410645 |
GC content
@ref | GC-content | method |
---|---|---|
8808 | 60.0 | |
67770 | 60 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 98 | no |
motile | no | 92.916 | no |
gram-positive | yes | 92.194 | no |
anaerobic | yes | 98.289 | yes |
halophile | no | 74.896 | no |
spore-forming | no | 95.302 | no |
thermophile | no | 93.02 | yes |
glucose-util | yes | 85.374 | no |
aerobic | no | 97.81 | yes |
flagellated | no | 96.052 | no |
glucose-ferment | yes | 81.574 | no |
External links
@ref: 8808
culture collection no.: DSM 20432, ATCC 27917, JCM 1211, BCRC 14677, CCUG 24608, CGMCC 1.2272, KCTC 3227, LMG 10736
straininfo link
- @ref: 71341
- straininfo: 1242
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 13130059 | Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov. | Zhu L, Li W, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.02617-0 | 2003 | Bifidobacterium/*classification/*genetics/metabolism, Chaperonin 60/*genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity | Genetics |
Phylogeny | 28714841 | Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). | Pechar R, Killer J, Salmonova H, Geigerova M, Svejstil R, Svec P, Sedlacek I, Rada V, Benada O | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001956 | 2017 | Aldehyde-Lyases/chemistry, Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Intestines/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sus scrofa/*microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8808 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20432) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20432 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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 | |||
71341 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1242.1 | StrainInfo: A central database for resolving microbial strain identifiers |