Strain identifier

BacDive ID: 1694

Type strain: Yes

Species: Bifidobacterium boum

Strain Designation: RU917

Strain history: ATCC 27917 <-- V. Scardovi RU 917.

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
78343species
1410645strain

strain history

@refhistory
8808<- ATCC <- V. Scardovi, RU917
67770ATCC 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

@refgrowthtypetemperaturerange
8808positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8808anaerobe
69480anaerobe99.446

spore formation

@refspore formationconfidence
69481no98
69480no99.999

murein

  • @ref: 8808
  • murein short key: A11.38
  • type: A4alpha L-Lys-D-Ser-D-Glu

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8808----------+++--------+---+--+-++---+++------------

Isolation, sampling and environmental information

isolation

@refsample type
8808bovine rumen
67770Rumen of cattle

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium boum strain DSM 20432 16S ribosomal RNA gene, partial sequenceGQ487635141ena78343
20218Bifidobacterium boum culture-collection DSM:20432 16S-23S ribosomal RNA intergenic spacer, partial sequenceJQ363654421ena78343
20218Bifidobacterium boum gene for 16S rRNA, partial sequence, strain: JCM 1211AB116287479ena78343
20218Bifidobacterium boum gene for 16S rRNA, partial sequence, strain: JCM 1211AB507082669ena78343
20218Bifidobacterium boum gene for 16S rRNA, partial sequence, strain: JCM 1211D861901517ena78343
20218Bifidobacterium boum strain KCTC 3227 16S ribosomal RNA gene, partial sequenceGU3618141481ena78343
67770Bifidobacterium boum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1211LC0717991421ena78343

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium boum DSM 204321410645.4wgspatric1410645
66792Bifidobacterium boum DSM 204321410645.3wgspatric1410645
66792Bifidobacterium boum strain LMG 1073678343.3wgspatric78343
66792Bifidobacterium boum LMG 107362600254979draftimg78343
66792Bifidobacterium boum DSM 204322681813198draftimg1410645
66792Bifidobacterium boum DSM 204322558860116draftimg1410645
67770Bifidobacterium boum DSM 20432GCA_000771385contigncbi1410645
67770Bifidobacterium boum LMG 10736GCA_000741535contigncbi78343
67770Bifidobacterium boum DSM 20432GCA_000687615scaffoldncbi1410645

GC content

@refGC-contentmethod
880860.0
6777060thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno92.916no
gram-positiveyes92.194no
anaerobicyes98.289yes
halophileno74.896no
spore-formingno95.302no
thermophileno93.02yes
glucose-utilyes85.374no
aerobicno97.81yes
flagellatedno96.052no
glucose-fermentyes81.574no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130059Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov.Zhu L, Li W, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.02617-02003Bifidobacterium/*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 SpecificityGenetics
Phylogeny28714841Bifidobacterium 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 OInt J Syst Evol Microbiol10.1099/ijsem.0.0019562017Aldehyde-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/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8808Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20432)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20432
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71341Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1242.1StrainInfo: A central database for resolving microbial strain identifiers