Strain identifier

BacDive ID: 1705

Type strain: Yes

Species: Bifidobacterium gallinarum

Strain Designation: Ch 206-5

Strain history: J. Watabe EBF 90/38 <-- T. Mitsuoka EBF 90/38 <-- E. M. Barnes EBF 90/38.

NCBI tax ID(s): 78344 (subspecies)

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General

@ref: 8992

BacDive-ID: 1705

DSM-Number: 20670

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

description: Bifidobacterium gallinarum Ch 206-5 is an anaerobe, mesophilic bacterium that was isolated from chicken cecum.

NCBI tax id

  • NCBI tax id: 78344
  • Matching level: subspecies

strain history

@refhistory
8992<- Y. Benno, Ch 206-5
67770J. Watabe EBF 90/38 <-- T. Mitsuoka EBF 90/38 <-- E. M. Barnes EBF 90/38.

doi: 10.13145/bacdive1705.20230509.8.1

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 gallinarum
  • full scientific name: Bifidobacterium gallinarum Watabe et al. 1983

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium pullorum subsp. gallinarum

@ref: 8992

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium gallinarum subsp. gallinarum

full scientific name: Bifidobacterium gallinarum subsp. gallinarum (Watabe et al. 1983) Liu et al. 2020

strain designation: Ch 206-5

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 8992
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
8992positivegrowth37mesophilic
52438positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8992anaerobe
52438anaerobe

murein

  • @ref: 8992
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase+
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase+3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52438C12:02.612
    52438C14:011.614
    52438C16:025.616
    52438C18:08.118
    52438C13:0 3OH/C15:1 i I/H6.214.469
    52438C13:1 at 12-132.112.931
    52438C16:1 ω7c0.915.819
    52438C16:1 ω9c3.215.774
    52438C17:0 anteiso0.816.722
    52438C17:0 iso 3OH2.518.161
    52438C17:1 ω5c ISO1.416.461
    52438C18:1 ω9c15.117.769
    52438C18:1 ω9c DMA9.518.226
    52438C18:2 ω6,9c/C18:0 ANTE4.917.724
    52438Unidentified0.810.908
    52438Unidentified1.212.467
    52438Unidentified0.916.278
    52438unknown 16.7542.916.754
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
52438--++-+++--++-+---++-++-+-+---

Isolation, sampling and environmental information

isolation

@refsample type
8992chicken cecum
52438Chicken caecum
67770Chicken cecum

isolation source categories

Cat1Cat2Cat3
#Host#Birds#Chicken
#Host Body-Site#Gastrointestinal tract#Large intestine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1595.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_39;97_1055;98_1260;99_1595&stattab=map
  • Last taxonomy: Bifidobacterium pullorum subclade
  • 16S sequence: LC071844
  • Sequence Identity:
  • Total samples: 42299
  • soil counts: 710
  • aquatic counts: 1025
  • animal counts: 40343
  • plant counts: 221

Safety information

risk assessment

  • @ref: 8992
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium gallinarum strain DSM 20670 16S ribosomal RNA gene, partial sequenceGQ487636129ena78344
20218Bifidobacterium gallinarum gene for 16S rRNA, partial sequence, strain: JCM 6291AB116302474ena78344
20218Bifidobacterium gallinarum gene for 16S rRNA, partial sequence, strain: JCM 6291AB507098654ena78344
20218Bifidobacterium gallinarum gene for 16S rRNA, partial sequence, strain: JCM 6291D861911509ena78344
20218Bifidobacterium gallinarum strain KCTC 3235 16S ribosomal RNA gene, partial sequenceGU3618211475ena78344
67770Bifidobacterium gallinarum gene for 16S ribosomal RNA, partial sequence, strain: JCM 6291LC0718441433ena78344

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium gallinarum DSM 206701437602.3wgspatric1437602
66792Bifidobacterium gallinarum strain LMG 1158678344.3wgspatric78344
66792Bifidobacterium pullorum gallinarum DSM 206702690316009draftimg1437602
66792Bifidobacterium pullorum gallinarum LMG 115862597490217draftimg78344
67770Bifidobacterium pullorum subsp. gallinarum DSM 20670GCA_000771505contigncbi1437602
67770Bifidobacterium pullorum subsp. gallinarum LMG 11586GCA_000741215contigncbi78344

GC content

@refGC-content
899266.4
6777064.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.667no
gram-positiveyes91.144no
anaerobicyes98.725yes
halophileno78.144no
spore-formingno95.809no
glucose-utilyes84.957no
thermophileno92.399yes
aerobicno97.783yes
flagellatedno96.849no
glucose-fermentyes81.418no

External links

@ref: 8992

culture collection no.: DSM 20670, ATCC 33777, CCUG 34990, JCM 6291, BCRC 14679, CGMCC 1.2283, KCTC 3235, LMG 11586

straininfo link

  • @ref: 71352
  • straininfo: 9636

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8992Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20670)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20670
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
52438Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34990)https://www.ccug.se/strain?id=34990
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/
68380Automatically annotated from API rID32A
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
71352Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9636.1StrainInfo: A central database for resolving microbial strain identifiers