Strain identifier

BacDive ID: 1732

Type strain: Yes

Species: Bifidobacterium gallicum

Strain Designation: P6

Strain history: CIP <- 1990, DSM <- H. Beerens: strain P6

NCBI tax ID(s): 561180 (strain), 78342 (species)

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General

@ref: 8519

BacDive-ID: 1732

DSM-Number: 20093

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

description: Bifidobacterium gallicum P6 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from intestine of adult.

NCBI tax id

NCBI tax idMatching level
561180strain
78342species

strain history

@refhistory
8519<- H. Beerens, P6
67770DSM 20093 <-- H. Beerens P6.
119509CIP <- 1990, DSM <- H. Beerens: strain P6

doi: 10.13145/bacdive1732.20250331.9.3

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 gallicum
  • full scientific name: Bifidobacterium gallicum Lauer 1990

@ref: 8519

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium gallicum

full scientific name: Bifidobacterium gallicum Lauer 1990 emend. Nouioui et al. 2018

strain designation: P6

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119509positiverod-shapedno
125438no93.5
125439no94.7

colony morphology

  • @ref: 119509
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8519BIFIDOBACTERIUM 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
40247MEDIUM 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)
119509CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
8519positivegrowth37
40247positivegrowth37
52429positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8519anaerobe
52429anaerobe
125439microaerophile95.6

murein

  • @ref: 8519
  • murein short key: A11.13
  • type: A3alpha L-Lys-L-Ala-L-Ser

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838017632nitrate-reduction
6838016634raffinose-fermentation
11950915824D-fructose+degradation
11950917634D-glucose+degradation
11950917057cellobiose-degradation
11950917716lactose-degradation
11950917306maltose-degradation
11950917814salicin+degradation
11950917992sucrose-degradation
1195094853esculin-hydrolysis
11950917632nitrate-reduction
11950916301nitrite-reduction
11950917632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
683714853esculin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6838027897tryptophan-energy source
6838029985L-glutamate-degradation
6838016024D-mannose-fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
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
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
6837112936D-galactose+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
6837117754glycerol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
11950935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
119509oxidase-
119509beta-galactosidase+3.2.1.23
119509gelatinase-
119509amylase+
119509DNase-
119509caseinase-3.4.21.50
119509catalase-1.11.1.6
119509tween esterase-
119509lecithinase-
119509lipase-
119509urease-3.5.1.5
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380alpha-galactosidase-3.2.1.22
68382beta-glucosidase+3.2.1.21
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase-3.4.11.2
68380phenylalanine arylamidase+
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52429C10:00.710
    52429C12:02.512
    52429C14:018.914
    52429C16:036.316
    52429C18:0418
    52429C13:0 3OH/C15:1 i I/H7.214.469
    52429C13:1 at 12-131.412.931
    52429C16:1 ω7c0.915.819
    52429C16:1 ω9c1.715.774
    52429C17:0 iso 3OH0.518.161
    52429C17:1 ω5c ISO116.461
    52429C17:1 ω9c0.816.773
    52429C18:1 ω9c13.917.769
    52429C18:2 ω6,9c/C18:0 ANTE4.617.724
    52429Unidentified4.718.221
    52429unknown 12.486112.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119509--++-+----++---++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8519----+++---+++--------+/---+/-++-+--+----++--+---------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
52429---+-++----------++-++-+-++-+

Isolation, sampling and environmental information

isolation

@refsample type
8519intestine of adult
52429Human adult intestine
67770Human feces
119509Human, Feces

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Gastrointestinal tract

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85191Risk group (German classification)
1195091Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium gallicum gene for 16S rRNA, partial sequence, strain: JCM 8224AB116301490nuccore561180
20218Bifidobacterium gallicum gene for 16S rRNA, partial sequence, strain: JCM 8224AB507097664nuccore561180
20218Bifidobacterium gallicum gene for 16S rRNA, partial sequence, strain: JCM 8224D861891530nuccore561180
20218Bifidobacterium gallicum strain KCTC 3277 16S ribosomal RNA gene, partial sequenceGU3618201495nuccore78342
67770Bifidobacterium gallicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 8224LC0718501482nuccore561180

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium gallicum DSM 20093561180.4wgspatric561180
66792Bifidobacterium gallicum DSM 20093 = LMG 11596561180.13wgspatric561180
66792Bifidobacterium gallicum DSM 20093 = LMG 11596561180.15wgspatric561180
66792Bifidobacterium gallicum DSM 200932671180475draftimg561180
66792Bifidobacterium gallicum DSM 20093, LMG 115962597490252draftimg561180
66792Bifidobacterium gallicum DSM 20093, LMG 115962562617144draftimg561180
67770Bifidobacterium gallicum DSM 20093 = LMG 11596GCA_000173375contigncbi561180
67770Bifidobacterium gallicum DSM 20093 = LMG 11596GCA_000771165contigncbi561180
67770Bifidobacterium gallicum DSM 20093 = LMG 11596GCA_000741205contigncbi561180

GC content

@refGC-contentmethod
851961.0thermal denaturation, midpoint method (Tm)
6777061

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes85.337no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes85.575no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.434no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no92.043no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.5yes
125438motile2+flagellatedAbility to perform flagellated movementno93.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno66.4
125439BacteriaNetmotilityAbility to perform movementno94.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive86.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile95.6

External links

@ref: 8519

culture collection no.: DSM 20093, ATCC 49850, JCM 8224, CCUG 34979, CGMCC 1.2274, CIP 103417, KCTC 3277, LMG 11596

straininfo link

  • @ref: 71379
  • straininfo: 9635

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2223594Bifidobacterium gallicum sp. nov. isolated from human feces.Lauer EInt J Syst Bacteriol10.1099/00207713-40-1-1001990Amino Acid Sequence, Bifidobacterium/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, Feces/*microbiology, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Sequence Homology, Nucleic AcidPathogenicity
Phylogeny20547379Characterization of an insertion sequence-like element, ISBlo15, identified in a size-increased cryptic plasmid pBK283 in Bifidobacterium longum BK28.Fukiya S, Sugiyama T, Kano Y, Yokota AJ Biosci Bioeng10.1016/j.jbiosc.2010.02.0132010Base Sequence, Bifidobacterium/*classification/*genetics, DNA Transposable Elements/*genetics, DNA, Bacterial/*genetics, Molecular Sequence Data, Plasmids/*genetics, Species SpecificityGenetics
Phylogeny30789326Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov.Duranti S, Lugli GA, Napoli S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura MInt J Syst Evol Microbiol10.1099/ijsem.0.0033062019Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification, Callithrix/*microbiology, DNA, Bacterial/genetics, Feces/microbiology, Genes, Bacterial, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rodentia/*microbiology, Saimiri/*microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8519Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20093)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20093
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
40247Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15213
52429Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34979)https://www.ccug.se/strain?id=34979
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
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
71379Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9635.1StrainInfo: A central database for resolving microbial strain identifiers
119509Curators of the CIPCollection of Institut Pasteur (CIP 103417)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103417
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