Strain identifier

BacDive ID: 132910

Type strain: Yes

Species: Veillonella tobetsuensis

Strain Designation: B16

Strain history: F. Nakazawa B16.

NCBI tax ID(s): 1110546 (species)

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General

@ref: 24698

BacDive-ID: 132910

DSM-Number: 104750

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, coccus-shaped

description: Veillonella tobetsuensis B16 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from tongue biofilm of healthy human adult .

NCBI tax id

  • NCBI tax id: 1110546
  • Matching level: species

strain history

@refhistory
24698<- JCM; JCM 17976 <- F. Nakazawa; B16
67770F. Nakazawa B16.

doi: 10.13145/bacdive132910.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Veillonellales
  • family: Veillonellaceae
  • genus: Veillonella
  • species: Veillonella tobetsuensis
  • full scientific name: Veillonella tobetsuensis Mashima et al. 2013

@ref: 24698

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Veillonellaceae

genus: Veillonella

species: Veillonella tobetsuensis

full scientific name: Veillonella tobetsuensis Mashima et al. 2013

strain designation: B16

type strain: yes

Morphology

cell morphology

  • @ref: 30703
  • gram stain: negative
  • cell length: 0.5 µm
  • cell width: 0.5 µm
  • cell shape: coccus-shaped
  • motility: no

pigmentation

  • @ref: 30703
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24698COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
24698PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104; with strain-specific modifications) 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 Sodium lactate 2.5 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 Vitamin K1 NaOH Tween 80 Distilled water

culture temp

@refgrowthtypetemperaturerange
24698positivegrowth37mesophilic
30703positiveoptimum37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30703
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 30703
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3070317632nitrate+reduction
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
30703acid phosphatase+3.1.3.2
30703alkaline phosphatase+3.1.3.1
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24698--------------+-------+------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24698tongue biofilm of healthy human adult (26 years)Health Sciences University of HokkaidoJapanJPNAsia
67770Tongue biofilm of healthy human adults

isolation source categories

Cat1Cat2Cat3
#Environmental#Biofilm
#Host#Human
#Host Body-Site#Oral cavity and airways#Mouth

Safety information

risk assessment

  • @ref: 24698
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24698
  • description: Veillonella tobetsuensis gene for 16S ribosomal RNA, partial sequence
  • accession: AB679109
  • length: 1520
  • database: ena
  • NCBI tax ID: 1110546

Genome sequences

  • @ref: 67770
  • description: Veillonella tobetsuensis ATCC BAA-2400
  • accession: GCA_001078375
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1110546

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.477yes
flagellatedno96.789no
gram-positiveno93.495yes
anaerobicyes99.662yes
aerobicno97.558yes
halophileno83.666no
spore-formingno89.364no
glucose-utilyes53.775no
thermophileno97.536yes
glucose-fermentno54.321no

External links

@ref: 24698

culture collection no.: DSM 104750, ATCC BAA 2400, JCM 17976

straininfo link

  • @ref: 91188
  • straininfo: 404308

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22843723Veillonella tobetsuensis sp. nov., an anaerobic, gram-negative coccus isolated from human tongue biofilms.Mashima I, Kamaguchi A, Miyakawa H, Nakazawa FInt J Syst Evol Microbiol10.1099/ijs.0.042515-02012Adult, Bacterial Typing Techniques, Biofilms, DNA, Bacterial/genetics, Fatty Acids/analysis, Humans, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tongue/*microbiology, Veillonella/*classification/genetics/isolation & purification, Young AdultPathogenicity
Phylogeny23664905Identification of Veillonella tobetsuensis in tongue biofilm by using a species-specific primer pair.Mashima I, Nakazawa FAnaerobe10.1016/j.anaerobe.2013.04.0152013Bacterial Proteins/*genetics, Base Sequence, *Biofilms, DNA Primers, DNA, Bacterial/chemistry/isolation & purification, Female, HSP70 Heat-Shock Proteins/*genetics, Humans, Male, Polymerase Chain Reaction, Species Specificity, Tongue/*microbiology, Veillonella/*classification/genetics/*isolation & purification, Young AdultEnzymology

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24698Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104750Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104750)
30703Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172703428776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
91188Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404308.1