Strain identifier

BacDive ID: 1701

Type strain: Yes

Species: Bifidobacterium cuniculi

Strain Designation: RA93, RA 93

Strain history: CIP <- 1990, DSM <- ATCC <- V. Scardoni: strain RA 93

NCBI tax ID(s): 1437601 (strain), 1688 (species)

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General

@ref: 8811

BacDive-ID: 1701

DSM-Number: 20435

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Bifidobacterium cuniculi RA93 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from rabbit faeces.

NCBI tax id

NCBI tax idMatching level
1437601strain
1688species

strain history

@refhistory
8811<- ATCC <- V. Scardovi, RA93
67770ATCC 27916 <-- V. Scardovi RA93.
118814CIP <- 1990, DSM <- ATCC <- V. Scardoni: strain RA 93

doi: 10.13145/bacdive1701.20230509.8.1

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 cuniculi
  • full scientific name: Bifidobacterium cuniculi Scardovi et al. 1979 (Approved Lists 1980)

@ref: 8811

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium cuniculi

full scientific name: Bifidobacterium cuniculi Scardovi et al. 1979 emend. Nouioui et al. 2018

strain designation: RA93, RA 93

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8811BIFIDOBACTERIUM 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
34255MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
118814CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8811positivegrowth37mesophilic
34255positivegrowth37mesophilic
47995positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8811anaerobe
47995anaerobe
69480anaerobe99.292

spore formation

@refspore formationconfidence
69481no100
69480no99.998

murein

  • @ref: 8811
  • murein short key: A11.21
  • type: A3alpha L-Lys(L-Orn)-L-Ala(L-Ser)-L-Ala2

Isolation, sampling and environmental information

isolation

@refsample typesampling date
8811rabbit faeces
47995Rabbit feces1989-05-02
67770Feces of a rabbit
118814Animal, Rabbit, feces

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Leporidae (Rabbit/Hare)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6013.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_2870;97_3527;98_4463;99_6013&stattab=map
  • Last taxonomy: Bifidobacterium cuniculi subclade
  • 16S sequence: LC071801
  • Sequence Identity:
  • Total samples: 5656
  • soil counts: 140
  • aquatic counts: 90
  • animal counts: 5399
  • plant counts: 27

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88111Risk group (German classification)
1188141Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium cunniculi 16S ribosomal RNAM587341487ena1688
20218Bifidobacterium cuniculi ATCC 27916 16S-23S intergenic spacer, partial sequenceU09790490ena1688
20218Bifidobacterium cuniculi gene for 16S rRNA, partial sequence, strain: JCM 1213AB116298489ena1688
20218Bifidobacterium cuniculi gene for 16S rRNA, partial sequence, strain: JCM 1213AB507094667ena1688
20218Bifidobacterium cuniculi strain KCTC 3276 16S ribosomal RNA gene, partial sequenceGU3618181492ena1688
20218Bifidobacterium cuniculi strain LMG 10738 16S ribosomal RNA gene, partial sequenceJX9869641481ena1688
8811Bifidobacterium cuniculi DSM 20435, whole genome shotgun sequencing projectJDUL00000000264ena1437601
67770Bifidobacterium cuniculi gene for 16S rRNA, partial sequenceAB4382231521ena1688
67770Bifidobacterium cuniculi gene for 16S ribosomal RNA, partial sequence, strain: JCM 1213LC0718011429ena1688

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium cuniculi DSM 204351437601.3wgspatric1437601
66792Bifidobacterium cuniculi strain LMG 107381688.3wgspatric1688
66792Bifidobacterium cuniculi LMG 107382597490228draftimg1688
66792Bifidobacterium cuniculi DSM 204352671180748draftimg1437601
67770Bifidobacterium cuniculi DSM 20435GCA_000771465contigncbi1437601
67770Bifidobacterium cuniculi LMG 10738GCA_000741575contigncbi1688

GC content

@refGC-contentmethod
881164.1
6777064.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.379no
gram-positiveyes92.106no
anaerobicyes97.493yes
halophileno76.9no
spore-formingno95.346no
thermophileno97.262yes
glucose-utilyes88.979no
aerobicno96.467yes
flagellatedno96.946no
glucose-fermentyes80.583no

External links

@ref: 8811

culture collection no.: DSM 20435, ATCC 27916, CCUG 24610, JCM 1213, BCRC 14672, CGMCC 1.2239, CIP 103379, KCTC 3276, LMG 10738

straininfo link

  • @ref: 71348
  • straininfo: 1247

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8811Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20435)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20435
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
34255Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15170
47995Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24610)https://www.ccug.se/strain?id=24610
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/
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
71348Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1247.1StrainInfo: A central database for resolving microbial strain identifiers
118814Curators of the CIPCollection of Institut Pasteur (CIP 103379)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103379