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Strain identifier

BacDive ID: 1726

Type strain: Yes

Species: Bifidobacterium merycicum

Strain Designation: Ru915B

Strain history: B. Biavati Ru915B.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2697

BacDive-ID: 1726

DSM-Number: 6492

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

description: Bifidobacterium merycicum Ru915B is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from rumen of cattle.

NCBI tax id

NCBI tax idMatching level
78345species
1410646strain

strain history

doi: 10.13145/bacdive1726.20221219.7.1

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

@ref: 2697

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium merycicum

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

strain designation: Ru915B

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
23364positive2.0-5.0 µmrod-shapedno
69480positive91.594

colony morphology

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2697BIFIDOBACTERIUM 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
2697positivegrowth37mesophilic
23364nogrowth25mesophilic
23364nogrowth>45thermophilic
23364positiveoptimum38-42
52428positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
23364positiveoptimum6.5-6.9
23364nogrowth4.5
23364nogrowth8.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2697anaerobe
23364anaerobe
52428anaerobe
69480anaerobe97.794

spore formation

@refspore formationconfidence
23364no
69480no99.471

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 98.728

murein

  • @ref: 2697
  • murein short key: A11.32
  • type: A4alpha L-Lys(L-Orn)-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336424265gluconate-builds acid from
2336429864mannitol-builds acid from
233646731melezitose-builds acid from
2336424265gluconate-fermentation
2336417754glycerol-fermentation
2336424996lactate-fermentation
2336429864mannitol-fermentation
2336437684mannose-fermentation
233646731melezitose-fermentation
2336426546rhamnose-fermentation
2336430911sorbitol-fermentation
2336427082trehalose-fermentation
2336417632nitrate-reduction
2336435581indole-
2336417272propionate-
2336417057cellobiose+builds acid from
2336416988D-ribose+builds acid from
2336465327D-xylose+builds acid from
2336430849L-arabinose+builds acid from
2336422599arabinose+fermentation
2336423652dextrin+fermentation
2336428260galactose+fermentation
2336417234glucose+fermentation
2336417716lactose+fermentation
2336417306maltose+fermentation
2336428053melibiose+fermentation
2336416634raffinose+fermentation
2336433942ribose+fermentation
2336428017starch+fermentation
2336417992sucrose+fermentation
2336418222xylose+fermentation
2336415443inulin+/-builds acid from
2336417814salicin+/-builds acid from
2336417057cellobiose+/-fermentation
2336428757fructose+/-fermentation
2336415443inulin+/-fermentation
2336417814salicin+/-fermentation

enzymes

  • @ref: 23364
  • value: catalase
  • activity: -
  • ec: 1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52428C10:0310
    52428C12:011.312
    52428C14:016.314
    52428C16:017.316
    52428C18:02.718
    52428C13:0 3OH/C15:1 i I/H2.314.469
    52428C13:1 at 12-130.612.931
    52428C16:0 3OH0.617.52
    52428C16:1 ω9c10.415.774
    52428C17:1 ω5c ISO0.716.461
    52428C17:1 ω9c0.916.773
    52428C18:1 ω9c22.217.769
    52428C18:2 ω6,9c/C18:0 ANTE4.717.724
    52428Unidentified0.612.472
    52428Unidentified113.768
    52428Unidentified4.718.225
    52428Unidentified0.719.297
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample type
2697rumen of cattle
52428Cattle rumen
67770Bovine rumen

isolation source categories

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

Safety information

risk assessment

  • @ref: 2697
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium merycicum strain DSM 6492 16S ribosomal RNA gene, partial sequenceGQ487639137ena78345
20218Bifidobacterium merycicum gene for 16S rRNA, partial sequence, strain: JCM 8219AB116324435ena78345
20218Bifidobacterium merycicum gene for 16S rRNA, partial sequence, strain: JCM 8219AB507128840ena78345
20218Bifidobacterium merycicum gene for 16S rRNA, partial sequence, strain: JCM 8219D861921435ena78345
20218Bifidobacterium merycicum strain KCTC 3369 16S ribosomal RNA gene, partial sequenceGU3618251480ena78345
67770Bifidobacterium merycicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 8219LC0718471392ena78345

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium merycicum DSM 64921410646.3wgspatric1410646
66792Bifidobacterium merycicum DSM 64921410646.5wgspatric1410646
66792Bifidobacterium merycicum strain LMG 1134178345.3wgspatric78345
66792Bifidobacterium merycicum DSM 64922660238375draftimg1410646
66792Bifidobacterium merycicum DSM 64922563366502draftimg1410646
66792Bifidobacterium merycicum LMG 113412600254980draftimg78345
67770Bifidobacterium merycicum DSM 6492 DSM 6492GCA_900129045contigncbi1410646
67770Bifidobacterium merycicum DSM 6492 DSM 6492GCA_000770945contigncbi1410646
67770Bifidobacterium merycicum LMG 11341GCA_000741615contigncbi78345
66792Pseudoxanthomonas winnipegensis NML 171200GCA_004284655contigpatric2480810
66792Yersinia vastinensis IP38831GCA_902170295contigpatric2890318
66792Yersinia proxima IP38663GCA_902170895contigpatric2890316

GC content

@refGC-contentmethod
269759.0thermal denaturation, midpoint method (Tm)
2336459.0Thermal denaturation, fluorometry
6777059thermal denaturation, midpoint method (Tm)

External links

@ref: 2697

culture collection no.: DSM 6492, ATCC 49391, CCUG 34976, JCM 8219, CGMCC 1.2273, KCTC 3369, KCTC 3423, LMG 11341

straininfo link

@refpassport
20218http://www.straininfo.net/strains/56135
20218http://www.straininfo.net/strains/56132

literature

  • topic: Phylogeny
  • Pubmed-ID: 1995032
  • title: Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle.
  • authors: Biavati B, Mattarelli P
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-41-1-163
  • year: 1991
  • mesh: Animals, 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 Topic
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2697Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6492)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6492
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
52428Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34976)https://www.ccug.se/strain?id=34976
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/
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)