Strain identifier

BacDive ID: 1711

Type strain: Yes

Species: Bifidobacterium magnum

Strain Designation: RA3

Strain history: ATCC 27540 <-- V. Scardovi RA3.

NCBI tax ID(s): 1121108 (strain), 1692 (species)

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General

@ref: 8640

BacDive-ID: 1711

DSM-Number: 20222

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

description: Bifidobacterium magnum RA3 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from rabbit faeces.

NCBI tax id

NCBI tax idMatching level
1692species
1121108strain

strain history

@refhistory
8640<- V. Scardovi, RA3
67770ATCC 27540 <-- V. Scardovi RA3.

doi: 10.13145/bacdive1711.20230509.8.1

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 magnum
  • full scientific name: Bifidobacterium magnum Scardovi and Zani 1974 (Approved Lists 1980)

@ref: 8640

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium magnum

full scientific name: Bifidobacterium magnum Scardovi and Zani 1974 emend. Nouioui et al. 2018

strain designation: RA3

type strain: yes

Morphology

cell morphology

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

Culture and growth conditions

culture medium

  • @ref: 8640
  • 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
8640positivegrowth37mesophilic
52436positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8640anaerobe
52436anaerobe
69480anaerobe98.769

spore formation

@refspore formationconfidence
69481no100
69480no100

murein

  • @ref: 8640
  • murein short key: A11.11
  • type: A3alpha L-Lys(L-Orn)-L-Ala2-L-Ser

Isolation, sampling and environmental information

isolation

@refsample type
8640rabbit faeces
52436Rabbit feces
67770Rabbit feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1053.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16205;96_606;97_709;98_827;99_1053&stattab=map
  • Last taxonomy: Bifidobacterium magnum subclade
  • 16S sequence: LC071819
  • Sequence Identity:
  • Total samples: 15552
  • soil counts: 140
  • aquatic counts: 147
  • animal counts: 15246
  • plant counts: 19

Safety information

risk assessment

  • @ref: 8640
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium magnum 16S ribosomal RNAM587401484ena1692
20218Bifidobacterium magnum ATCC 27540 16S rRNA-23S rRNA intergenic spacerU09878391ena1692
20218Bifidobacterium magnum gene for 16S rRNA, partial sequence, strain: JCM 1218AB116321487ena1692
20218Bifidobacterium magnum gene for 16S rRNA, partial sequence, strain: JCM 1218AB507125674ena1692
20218Bifidobacterium magnum gene for 16S rRNA, partial sequence, strain: JCM 1218D861931525ena1692
20218Bifidobacterium magnum strain KCTC 3228 16S ribosomal RNA gene, partial sequenceGU3618241488ena1692
67770Bifidobacterium magnum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1218LC0718191434ena1692

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium magnum DSM 202221121108.4wgspatric1121108
66792Bifidobacterium magnum DSM 202221121108.3wgspatric1121108
66792Bifidobacterium magnum strain LMG 115911692.3wgspatric1692
66792Bifidobacterium magnum DSM 202222695420660draftimg1121108
66792Bifidobacterium magnum LMG 115912597490218draftimg1692
66792Bifidobacterium magnum DSM 202222524023203draftimg1121108
67770Bifidobacterium magnum DSM 20222GCA_000420565contigncbi1121108
67770Bifidobacterium magnum DSM 20222GCA_000771365contigncbi1121108
67770Bifidobacterium magnum LMG 11591GCA_000741255contigncbi1692

GC content

@refGC-contentmethod
864060.0
6777060thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.842no
flagellatedno96.842no
gram-positiveyes93.714no
anaerobicyes95.853yes
aerobicno96.826no
halophileno64.437no
spore-formingno97.245no
thermophileno95.898yes
glucose-utilyes87.815no
glucose-fermentyes86.751no

External links

@ref: 8640

culture collection no.: DSM 20222, ATCC 27540, CCUG 34987, JCM 1218, BCRC 14676, CGMCC 1.2189, HAMBI 569, KCTC 3228, LMG 11591

straininfo link

  • @ref: 71358
  • straininfo: 9644

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8640Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20222)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20222
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
52436Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34987)https://www.ccug.se/strain?id=34987
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
71358Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9644.1StrainInfo: A central database for resolving microbial strain identifiers