Strain identifier

BacDive ID: 1706

Type strain: Yes

Species: Bifidobacterium globosum

Strain Designation: RU224

Strain history: ATCC 25865 <-- V. Scardovi RU 224.

NCBI tax ID(s): 1690 (subspecies)

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General

@ref: 8518

BacDive-ID: 1706

DSM-Number: 20092

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Bifidobacterium globosum RU224 is an anaerobe, mesophilic bacterium that was isolated from rumen.

NCBI tax id

  • NCBI tax id: 1690
  • Matching level: subspecies

strain history

@refhistory
8518<- V. Scardovi, RU224
67770ATCC 25865 <-- V. Scardovi RU 224.

doi: 10.13145/bacdive1706.20250331.9.3

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 globosum
  • full scientific name: Bifidobacterium globosum (ex Scardovi et al. 1969) Biavati et al. 1982

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium pseudolongum subsp. globosum

@ref: 8518

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium globosum

full scientific name: Bifidobacterium globosum (ex Scardovi et al. 1969) Biavati et al. 1982 emend. Nouioui et al. 2018

strain designation: RU224

type strain: yes

Morphology

cell morphology

  • @ref: 125438
  • motility: no
  • confidence: 94

Culture and growth conditions

culture medium

  • @ref: 8518
  • 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

@refgrowthtypetemperature
8518positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 8518
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 90.277

murein

  • @ref: 8518
  • murein short key: A21.02
  • type: A3ß L-Orn(L-Lys)-L-Ala2-3

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117754glycerol-builds acid from
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
6837117716lactose-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
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-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
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8518-----+----+/-++-----------+--++------+++------------

Isolation, sampling and environmental information

isolation

@refsample type
8518rumen
67770Rumen

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Organ
  • Cat3: #Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_2281.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_1232;97_1460;98_1781;99_2281&stattab=map
  • Last taxonomy: Bifidobacterium pseudolongum subclade
  • 16S sequence: LC071834
  • Sequence Identity:
  • Total samples: 83989
  • soil counts: 858
  • aquatic counts: 870
  • animal counts: 81910
  • plant counts: 351

Safety information

risk assessment

  • @ref: 8518
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium globosum 16S ribosomal RNAM587361488nuccore1690
20218Bifidobacterium globosum ATCC25865 16S-23S intergenic spacerU09524548nuccore1690
20218Bifidobacterium pseudolongum subsp. globosum strain DSM 20092 16S ribosomal RNA gene, partial sequenceGQ487637146nuccore1690
20218Bifidobacterium pseudocatenulatum gene for 16S rRNA, partial sequence, strain: JCM 5820AB116329480nuccore28026
20218Bifidobacterium pseudolongum subsp. globosum gene for 16S rRNA, partial sequence, strain: JCM 5820AB116332488nuccore1690
20218Bifidobacterium pseudolongum subsp. globosum gene for 16S rRNA, partial sequence, strain: JCM 5820AB507138693nuccore1690
20218Bifidobacterium pseudolongum subsp. globosum JCM 5820 gene for 16S rRNA, partial sequenceD861941528nuccore1690
20218Bifidobacterium pseudolongum subsp. globosum strain KCTC 3234 16S ribosomal RNA gene, partial sequenceGU3618281491nuccore1690
67770Bifidobacterium pseudolongum subsp. globosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 5820LC0718341407nuccore1690

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium pseudolongum subsp. globosum DSM 20092GCA_002706665completencbi1410605
66792Bifidobacterium pseudolongum subsp. globosum DSM 20092GCA_000771145contigncbi1410605
66792Bifidobacterium pseudolongum subsp. globosum LMG 11569GCA_000741295contigncbi1690
66792Bifidobacterium pseudolongum subsp. globosum DSM 200921410605.4wgspatric1410605
66792Bifidobacterium pseudolongum subsp. globosum DSM 200921410605.3wgspatric1410605
66792Bifidobacterium pseudolongum subsp. globosum DSM 20092 strain DSM200921410605.6completepatric1410605
66792Bifidobacterium pseudolongum subsp. globosum strain LMG 115691690.4wgspatric1690
66792Bifidobacterium pseudolongum globosum DSM 200922690316232draftimg1410605
66792Bifidobacterium pseudolongum globosum DSM 200922823497638completeimg1410605
66792Bifidobacterium pseudolongum globosum LMG 115692597490251draftimg1690
66792Bifidobacterium pseudolongum globosum DSM 200922558860115draftimg1410605
67770Bifidobacterium pseudolongum subsp. globosum DSM 20092GCA_000687595contigncbi1410605

GC content

@refGC-contentmethod
851863.8
6777063.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes87.009no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes82.501yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.586yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.277no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94yes
125438motile2+flagellatedAbility to perform flagellated movementno94no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno83.6
125439BacteriaNetmotilityAbility to perform movementno80
125439BacteriaNetgram_stainReaction to gram-stainingpositive89.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe61.5

External links

@ref: 8518

culture collection no.: DSM 20092, ATCC 25865, JCM 5820, BCRC 14663, CCUG 34978, CCUG 39904, CGMCC 1.2203, KCTC 3234, LMG 10509, LMG 11569, NCFB 2245

straininfo link

  • @ref: 71353
  • straininfo: 9637

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8518Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20092)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20092
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
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
71353Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9637.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1