Strain identifier

BacDive ID: 1704

Type strain: Yes

Species: Bifidobacterium dentium

Strain Designation: B764

Strain history: CIP <- 1994, ATCC <- V. Scardovi: strain B764

NCBI tax ID(s): 1150423 (strain), 1689 (species)

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General

@ref: 8812

BacDive-ID: 1704

DSM-Number: 20436

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

description: Bifidobacterium dentium B764 is an anaerobe, mesophilic bacterium that was isolated from dental caries.

NCBI tax id

NCBI tax idMatching level
1689species
1150423strain

strain history

@refhistory
8812<- ATCC; ATCC 27534 <- V. Scardovi; B764
67770ATCC 27534 <-- V. Scardovi B764.
118913CIP <- 1994, ATCC <- V. Scardovi: strain B764

doi: 10.13145/bacdive1704.20230509.8.1

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 dentium
  • full scientific name: Bifidobacterium dentium Scardovi and Crociani 1974 (Approved Lists 1980)

@ref: 8812

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium dentium

full scientific name: Bifidobacterium dentium Scardovi and Crociani 1974 emend. Nouioui et al. 2018

strain designation: B764

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8812BIFIDOBACTERIUM 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
34556MEDIUM 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)
8812COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
118913CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8812positivegrowth37mesophilic
34556positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 8812
  • oxygen tolerance: anaerobe

murein

  • @ref: 8812
  • murein short key: A11.32
  • type: A4alpha L-Lys(L-Orn)-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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
68367trehalose+builds acid from27082
68367L-rhamnose+builds acid from62345
68367sorbitol+builds acid from30911
68367raffinose+builds acid from16634
68367melezitose+builds acid from6731
68367D-mannose+builds acid from16024
68367cellobiose+builds acid from17057
68367glycerol+builds acid from17754
68367esculin+hydrolysis4853
68367gelatin-hydrolysis5291
68367L-arabinose+builds acid from30849
68367D-xylose+builds acid from65327
68367salicin+builds acid from17814
68367maltose+builds acid from17306
68367sucrose+builds acid from17992
68367lactose+builds acid from17716
68367D-mannitol+builds acid from16899
68367D-glucose+builds acid from17634
68367urea-hydrolysis16199
68367tryptophan-energy source27897
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose+fermentation16024
68380raffinose+fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
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
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
8812--++++++++-+++++++++

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8812----+++---++++----+--+-+++++++++---+++-++---------
8812----+++---++++----+--+-+++++++++---+++-++------++-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8812--++-+++--++-----++-++/--+-++-+/-

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
8812dental caries
67770Dental caries
118913Human, Dental caries1969

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways
  • Cat3: #Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_1623.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_920;97_1072;98_1281;99_1623&stattab=map
  • Last taxonomy: Bifidobacterium dentium subclade
  • 16S sequence: LC071795
  • Sequence Identity:
  • Total samples: 101819
  • soil counts: 778
  • aquatic counts: 2127
  • animal counts: 98673
  • plant counts: 241

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88122Risk group (German classification)
1189131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium dentium gene for 16S rRNA, partial sequence, strain: ATCC 27534D861831520ena1150423
20218Bifidobacterium dentium ATCC 27534 16S-23S rRNA intergenic spacerU10434494ena1150423
20218Bifidobacterium dentium gene for 16S rRNA, partial sequence, strain: JCM 1195AB116299479ena1150423
20218Bifidobacterium dentium gene for 16S rRNA, partial sequence, strain: JCM 1195AB507095668ena1150423
20218Bifidobacterium dentium strain KCTC 3222 16S ribosomal RNA gene, partial sequenceGU3618191483ena1150423
67770Bifidobacterium dentium gene for 16S ribosomal RNA, partial sequence, strain: JCM 1195LC0717951420ena1150423

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium dentium NCTC11816GCA_900637175completencbi1689
66792Bifidobacterium dentium strain NCTC118161689.18completepatric1689
66792Bifidobacterium dentium DSM 204362816332288completeimg1150423
66792Bifidobacterium dentium DSM 204362634166294draftimg1150423
67770Bifidobacterium dentium JCM 1195 = DSM 20436GCA_001042595completencbi1150423
67770Bifidobacterium dentium JCM 1195 = DSM 20436GCA_900105745contigncbi1150423
67770Bifidobacterium dentium JCM 1195 = DSM 20436GCA_000771725contigncbi1150423

GC content

@refGC-contentmethod
881261.2
6777061.2thermal denaturation, midpoint method (Tm)

External links

@ref: 8812

culture collection no.: DSM 20436, ATCC 27534, JCM 1195, BCRC 14662, CCUG 17378, CCUG 18367, CECT 687, CGMCC 1.2188, CIP 104176, KCTC 3222, LMG 10506, NCFB 2243, NCTC 11816

straininfo link

  • @ref: 71351
  • straininfo: 1248

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21148680Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces.Morita H, Nakano A, Onoda H, Toh H, Oshima K, Takami H, Murakami M, Fukuda S, Takizawa T, Kuwahara T, Ohno H, Tanabe S, Hattori MInt J Syst Evol Microbiol10.1099/ijs.0.024521-02010Bacterial Proteins/genetics/metabolism, Base Composition, Bifidobacterium/*classification/genetics/*isolation & purification, Cellulases/genetics/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Feces/*microbiology, Humans, Infant, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, beta-Galactosidase/genetics/metabolismMetabolism
Genetics25858847Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195T, Isolated from Human Dental Caries.Toh H, Hayashi J, Oshima K, Nakano A, Takayama Y, Takanashi K, Morita H, Hattori MGenome Announc10.1128/genomeA.00284-152015Phylogeny
Cultivation27660160Acidogenicity of dual-species biofilms of bifidobacteria and Streptococcus mutans.de Matos BM, Brighenti FL, Do T, Beighton D, Koga-Ito CYClin Oral Investig10.1007/s00784-016-1958-12016Animals, Bifidobacterium/*growth & development, Biofilms/*growth & development, Cell Culture Techniques, Culture Media, Hydrogen-Ion Concentration, Lactobacillus acidophilus, Streptococcus mutans/*growth & development
Phylogeny33052806Bifidobacteria in two-toed sloths (Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov.Modesto M, Satti M, Watanabe K, Huang CH, Liou JS, Tamura T, Saito S, Mori K, Huang L, Sandri C, Spiezio C, Sgorbati B, Scarafile D, Camma C, Ancora M, Patavino C, Arita M, Mattarelli PInt J Syst Evol Microbiol10.1099/ijsem.0.0045062020Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Genes, Bacterial, Italy, Male, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sloths/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8812Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20436)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20436
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
34556Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16055
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/
68367Automatically annotated from API 20A
68371Automatically annotated from API 50CH acid
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
71351Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1248.1StrainInfo: A central database for resolving microbial strain identifiers
118913Curators of the CIPCollection of Institut Pasteur (CIP 104176)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104176