Strain identifier

BacDive ID: 1723

Type strain: Yes

Species: Bifidobacterium ruminantium

Strain Designation: Ru687

Strain history: B. Biavati Ru687.

NCBI tax ID(s): 1410647 (strain), 78346 (species)

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General

@ref: 2694

BacDive-ID: 1723

DSM-Number: 6489

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Bifidobacterium ruminantium Ru687 is an anaerobe, mesophilic, Gram-positive bacterium that forms irregular colonies and was isolated from rumen of cattle.

NCBI tax id

NCBI tax idMatching level
1410647strain
78346species

strain history

@refhistory
2694<- B. Biavati, Ru687
67770B. Biavati Ru687.

doi: 10.13145/bacdive1723.20230509.8.1

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 ruminantium
  • full scientific name: Bifidobacterium ruminantium Biavati and Mattarelli 1991

@ref: 2694

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium ruminantium

full scientific name: Bifidobacterium ruminantium Biavati and Mattarelli 1991 emend. Nouioui et al. 2018

strain designation: Ru687

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
23364positive3.0-6.0 µmrod-shapedno
69480no91.961
69480positive99.999

colony morphology

  • @ref: 23364
  • colony color: cream to white
  • colony shape: irregular
  • medium used: Trypticase-Phytone-yeast extract agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2694BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: 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
23364Trypticase-Phytone-yeast extract agaryes

culture temp

@refgrowthtypetemperaturerange
2694positivegrowth37mesophilic
23364nogrowth25mesophilic
23364nogrowth45thermophilic
23364positiveoptimum38-42
52427positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
23364positiveoptimum6.5-6.9
23364nogrowth4.5
23364nogrowth8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2694anaerobe
23364anaerobe
52427anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
23364no
69481no100
69480no99.992

murein

  • @ref: 2694
  • murein short key: A11.21
  • type: A3alpha L-Lys(L-Orn)-L-Ala(L-Ser)-L-Ala2

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336417057cellobiose-builds acid from
2336424265gluconate-builds acid from
2336415443inulin-builds acid from
2336430849L-arabinose-builds acid from
233646731melezitose-builds acid from
2336418222xylose-builds acid from
2336422599arabinose-fermentation
2336417057cellobiose-fermentation
2336424265gluconate-fermentation
2336417754glycerol-fermentation
2336415443inulin-fermentation
2336424996lactate-fermentation
2336437684mannose-fermentation
233646731melezitose-fermentation
2336426546rhamnose-fermentation
2336430911sorbitol-fermentation
2336427082trehalose-fermentation
2336418222xylose-fermentation
2336417632nitrate-reduction
2336435581indole-
2336417272propionate-
2336429864mannitol+builds acid from
2336433942ribose+builds acid from
2336423652dextrin+fermentation
2336428757fructose+fermentation
2336428260galactose+fermentation
2336417234glucose+fermentation
2336417716lactose+fermentation
2336417306maltose+fermentation
2336429864mannitol+fermentation
2336428053melibiose+fermentation
2336416634raffinose+fermentation
2336433942ribose+fermentation
2336428017starch+fermentation
2336417992sucrose+fermentation
2336417814salicin+/-builds acid from
2336417814salicin+/-fermentation
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52427C10:00.710
    52427C12:02.712
    52427C14:06.514
    52427C16:025.116
    52427C18:04.518
    52427C13:0 3OH/C15:1 i I/H2.214.469
    52427C16:1 ω7c0.815.819
    52427C16:1 ω9c1.715.774
    52427C17:0 2OH24.818.249
    52427C17:0 iso 3OH1.818.161
    52427C17:1 ISO I/C16:0 DMA0.816.481
    52427C17:1 ω9c3.916.773
    52427C18:1 ω9c19.717.769
    52427C18:2 ω6,9c/C18:0 ANTE4.417.724
    52427Unidentified0.412.472
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
2694-----+----+++-----+--+--+++-++++---+++------------
2694-----+----+++--------+--+++-+-++---+++------------

Isolation, sampling and environmental information

isolation

@refsample type
2694rumen of cattle
52427Cattle rumen
67770Bovine rumen

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_4682.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_920;97_1072;98_1898;99_4682&stattab=map
  • Last taxonomy: Bifidobacterium ruminantium
  • 16S sequence: LC071848
  • Sequence Identity:
  • Total samples: 59424
  • soil counts: 311
  • aquatic counts: 1061
  • animal counts: 57912
  • plant counts: 140

Safety information

risk assessment

  • @ref: 2694
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium ruminantium strain DSM 6489 16S ribosomal RNA gene, partial sequenceGQ438820358ena78346
20218Bifidobacterium ruminantium strain DSM 6489 16S ribosomal RNA gene, partial sequenceGQ487644154ena78346
20218Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222AB116347477ena78346
20218Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222AB507151796ena78346
20218Bifidobacterium ruminantium gene for 16S rRNA, partial sequence, strain: JCM 8222D861971437ena78346
20218Bifidobacterium ruminantium strain JCM 8222 16S ribosomal RNA gene, partial sequenceGQ227715317ena78346
20218Bifidobacterium ruminantium strain KCTC 3425 16S ribosomal RNA gene, partial sequenceGU3618311480ena78346
67770Bifidobacterium ruminantium gene for 16S ribosomal RNA, partial sequence, strain: JCM 8222LC0718481398ena78346

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium ruminantium DSM 64891410647.3wgspatric1410647
66792Bifidobacterium ruminantium DSM 64891410647.4wgspatric1410647
66792Bifidobacterium ruminantium strain LMG 2181178346.3wgspatric78346
66792Bifidobacterium ruminantium DSM 64892558860117draftimg1410647
66792Bifidobacterium ruminantium LMG 218112597490258draftimg78346
66792Bifidobacterium ruminantium DSM 64892657244954draftimg1410647
67770Bifidobacterium ruminantium DSM 6489GCA_000770925contigncbi1410647
67770Bifidobacterium ruminantium LMG 21811GCA_000741365contigncbi78346
67770Bifidobacterium ruminantium DSM 6489GCA_000687635contigncbi1410647

GC content

@refGC-contentmethod
269457.0thermal denaturation, midpoint method (Tm)
2336457.0Thermal denaturation, fluorometry
6777057thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.889yes
gram-positiveyes92.227yes
anaerobicyes98.42no
halophileno70.358no
spore-formingno94.879yes
glucose-utilyes87.667no
thermophileno95.569no
aerobicno97.725no
flagellatedno96.315yes
glucose-fermentyes85.68yes

External links

@ref: 2694

culture collection no.: DSM 6489, ATCC 49390, CCUG 34975, JCM 8222, CGMCC 1.2241, KCTC 3425, LMG 12588, LMG 21811

straininfo link

  • @ref: 71370
  • straininfo: 7859

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1995032Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle.Biavati B, Mattarelli PInt J Syst Bacteriol10.1099/00207713-41-1-1631991Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/cytology/isolation & purification/physiology, Cattle/*microbiology, DNA, Bacterial/analysis/genetics, Nucleic Acid Hybridization, Rumen/*microbiology, Sequence Homology, Nucleic Acid, Terminology as TopicEnzymology
Phylogeny20081020Bifidobacterium stercoris sp. nov., isolated from human faeces.Kim MS, Roh SW, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.019943-02010Adult, Aldehyde-Lyases/metabolism, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Male, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny24944342Bifidobacterium faecale sp. nov., isolated from human faeces.Choi JH, Lee KM, Lee MK, Cha CJ, Kim GBInt J Syst Evol Microbiol10.1099/ijs.0.063479-02014Aldehyde-Lyases/metabolism, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Infant, Newborn, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2694Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6489)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6489
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
23364B. BIAVATI, P. MATTARELLI10.1099/00207713-41-1-163Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the Rumens of CattleIJSEM 41: 163-168 19911995032
52427Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34975)https://www.ccug.se/strain?id=34975
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)
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
71370Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7859.1StrainInfo: A central database for resolving microbial strain identifiers