Strain identifier

BacDive ID: 1722

Type strain: No

Species: Bifidobacterium thermophilum

Strain Designation: RU 326

Strain history: DSM 20212 <-- V. Scardovi RU 326 ("Bifidobacterium ruminale").

NCBI tax ID(s): 1410648 (strain), 33905 (species)

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General

@ref: 8481

BacDive-ID: 1722

DSM-Number: 20212

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

description: Bifidobacterium thermophilum RU 326 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from bovine rumen.

NCBI tax id

NCBI tax idMatching level
1410648strain
33905species

strain history

@refhistory
8481<- V. Scardovi, RU 326 (Bifidobacterium ruminale)
67770DSM 20212 <-- V. Scardovi RU 326 ("Bifidobacterium ruminale").

doi: 10.13145/bacdive1722.20230509.8.1

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 thermophilum
  • full scientific name: Bifidobacterium thermophilum corrig. Mitsuoka 1969 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium thermophilium

@ref: 8481

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium thermophilum

full scientific name: Bifidobacterium thermophilum Mitsuoka 1969 emend. Nouioui et al. 2018

strain designation: RU 326

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 99.999

Culture and growth conditions

culture medium

  • @ref: 8481
  • 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
8481positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8481anaerobe
69480anaerobe99.45

spore formation

@refspore formationconfidence
69481no100
69480no99.998

murein

  • @ref: 8481
  • murein short key: A21.06
  • type: A4ß L-Orn(L-Lys)-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
8481----------+++--------+--+++-+-++---+++--+---------

Isolation, sampling and environmental information

isolation

@refsample type
8481bovine rumen
67770Bovine rumen

isolation source categories

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

Safety information

risk assessment

  • @ref: 8481
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium thermophilum DSM 202121410648.3wgspatric1410648
66792Bifidobacterium thermophilum DSM 202122558860129draftimg1410648
67770Bifidobacterium thermophilum DSM 20212GCA_000687575contigncbi1410648

GC content

  • @ref: 8481
  • GC-content: 60.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.536no
gram-positiveyes92.348no
anaerobicyes98.453yes
halophileno70.376no
spore-formingno96.241no
thermophileno93.901no
glucose-utilyes85.815no
aerobicno98.29yes
flagellatedno97.085no
glucose-fermentyes81.343no

External links

@ref: 8481

culture collection no.: DSM 20212, ATCC 25866, JCM 1268, KCTC 3471

straininfo link

  • @ref: 71369
  • straininfo: 92170

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology95384Immunological relationships among transaldolases in the genus Bifidobacterium.Sgorbati B, Scardovi VAntonie Van Leeuwenhoek10.1007/BF004007861979Actinomycetaceae/*classification/enzymology/immunology, Epitopes, Immunodiffusion, Isoenzymes/*immunology, Transaldolase/*immunology, Transferases/*immunologyPhylogeny
Metabolism10552858Binding of ferric iron to the cell walls and membranes of Bifidobacterium thermophilum: effect of free radicals.Kot E, Bezkorovainy AJ Agric Food Chem10.1021/jf990474l1999Aluminum/metabolism, Bifidobacterium/*metabolism, Cell Wall/*metabolism, Ferric Compounds/*metabolism, Free Radicals, Glucose/metabolism, Lipid Peroxidation
Metabolism11510661The effect of nisin on the physiology of Bifidobacterium thermophilum.Kot E, Murad Y, Bezkorovainy AJ Food Prot10.4315/0362-028x-64.8.12062001Anti-Bacterial Agents/*pharmacology, Bifidobacterium/drug effects/growth & development/*physiology, Ferric Compounds/*metabolism, Lactic Acid/metabolism, Nisin/*pharmacology, Time FactorsPhysiology

Reference

@idauthorscataloguedoi/urltitle
8481Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20212)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20212
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
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
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
71369Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92170.1StrainInfo: A central database for resolving microbial strain identifiers