Strain identifier

BacDive ID: 17174

Type strain: Yes

Species: Veillonella parvula

Strain Designation: Te3

Strain history: DSM 2008 <-- ATCC 10790 <-- J. E. Faber <-- A. R. Prévot Te3.

NCBI tax ID(s): 29466 (species)

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General

@ref: 956

BacDive-ID: 17174

DSM-Number: 2008

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

description: Veillonella parvula Te3 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from intestinal tract.

NCBI tax id

  • NCBI tax id: 29466
  • Matching level: species

strain history

@refhistory
956<- ATCC; ATCC 10790 <- J.E. Faber; <- A. R. Prevot; Te3
67770DSM 2008 <-- ATCC 10790 <-- J. E. Faber <-- A. R. Prévot Te3.

doi: 10.13145/bacdive17174.20230509.8.1

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 parvula
  • full scientific name: Veillonella parvula (Veillon and Zuber 1898) Prévot 1933 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Staphylococcus parvulus
    20215Veillonella alcalescens

@ref: 956

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Veillonellaceae

genus: Veillonella

species: Veillonella parvula subsp. parvula

full scientific name: Veillonella parvula subsp. parvula (Veillon and Zuber 1898) Rogosa 1965

strain designation: Te3

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.957

colony morphology

@reftype of hemolysisincubation period
956gamma1-2 days
448422-3 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_2008_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
956PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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
956VEILLONELLA MEDIUM (DSMZ Medium 136)yeshttps://mediadive.dsmz.de/medium/136Name: VEILLONELLA MEDIUM (DSMZ Medium 136) Composition: Na-(DL)-lactate 7.5 g/l Trypticase 5.0 g/l Yeast extract 3.0 g/l Glucose 1.0 g/l Na-thioglycolate 0.75 g/l Putrescine 0.003 g/l Resazurin 0.001 g/l Tween 80 Distilled water
956COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
956positivegrowth37mesophilic
44842positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
956anaerobe
44842anaerobe
69480anaerobe99.999

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.947

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-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-
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
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
956--------------+-------+/-------
956-+------------+-------+------
956--------------+--------------
956-+------------+--------------

Isolation, sampling and environmental information

isolation

@refsample type
956intestinal tract
44842Intestinal tract
67770Intestinal tract

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6475.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_39;96_80;97_84;98_1243;99_6475&stattab=map
  • Last taxonomy: Veillonella
  • 16S sequence: HM007566
  • Sequence Identity:
  • Total samples: 663
  • soil counts: 2
  • aquatic counts: 2
  • animal counts: 653
  • plant counts: 6

Safety information

risk assessment

  • @ref: 956
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Veillonella parvula gene for 16S ribosomal RNA, partial sequence, strain: JCM 12972AB5384371524ena29466
20218Veillonella parvula strain ATCC 10790 16S ribosomal RNA gene, partial sequenceAY9957671497ena479436
20218Veillonella parvula DSM 2008 16S ribosomal RNA gene, partial sequenceHM0075661345ena479436
20218V.parvula 16S rRNA geneX840051513ena479436

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Veillonella parvula NCTC11810GCA_900186885completencbi29466
66792Veillonella parvula DSM 2008GCA_000024945completencbi479436
66792Veillonella parvula DSM 2008479436.6completepatric479436
66792Veillonella parvula strain NCTC1181029466.62completepatric29466
66792Veillonella parvula Te3, DSM 2008646311965completeimg479436
66792Veillonella parvula NCTC 118102814123216completeimg29466

GC content

@refGC-contentmethod
95638.0
6777038thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
flagellatedno95.782no
gram-positiveno93.875no
anaerobicyes99.49yes
aerobicno97.66yes
halophileno84.883no
spore-formingno89.187no
thermophileno99.114yes
glucose-utilyes51.075no
motileno91.36no
glucose-fermentno51.559no

External links

@ref: 956

culture collection no.: CCUG 5123, ATCC 17742, DSM 2008, ATCC 10790, JCM 12972, NCTC 11810

straininfo link

  • @ref: 86173
  • straininfo: 264272

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Enzymology1775087Biological effects of Veillonella parvula and Bacteroides intermedius lipopolysaccharides.Matera G, Liberto MC, Berlinghieri MC, Foca AMicrobiologica1991Animals, *Bacteroides, Body Weight/drug effects, Dose-Response Relationship, Drug, Drinking/drug effects, Electrophoresis, Polyacrylamide Gel, Escherichia coli, Lethal Dose 50, Lipopolysaccharides/isolation & purification/*toxicity, Male, Mice, Mice, Inbred C57BL, Salmonella typhimurium, *VeillonellaPathogenicity
Lipids7056696Effects of growth temperature on fatty acid and alk-1-enyl group compositions of Veillonella parvula and Megasphaera elsdenii phospholipids.Johnston NC, Goldfine HJ Bacteriol1982Fatty Acids/analysis, Membrane Lipids/analysis, Phosphatidylethanolamines/analysis, Phosphatidylserines/analysis, Phospholipids/*analysis, Plasmalogens/*analysis, Temperature, Veillonella/*analysis/growth & development, Veillonellaceae/*analysis/growth & development10.1128/jb.149.2.567-575.1982
Enzymology7251145Identification of a Streptococcus salivarius cell wall component mediating coaggregation with Veillonella alcalescens V1.Weerkamp AH, McBride BCInfect Immun1981Bacterial Proteins/*physiology, Cell Wall/analysis, Electrophoresis, Polyacrylamide Gel, Glycoproteins/*physiology, Immunoelectrophoresis, Isoelectric Focusing, Streptococcus/*analysis/physiology/ultrastructure, Veillonella/*physiology10.1128/iai.32.2.723-730.1981
Phylogeny18319459Veillonella rogosae sp. nov., an anaerobic, Gram-negative coccus isolated from dental plaque.Arif N, Do T, Byun R, Sheehy E, Clark D, Gilbert SC, Beighton DInt J Syst Evol Microbiol2008Anaerobiosis, Bacterial Proteins/genetics, Bacterial Typing Techniques, Child, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, DNA-Directed RNA Polymerases/genetics, Dental Plaque/*microbiology, Genes, rRNA, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Veillonella/*classification/genetics/*isolation & purification/physiologyPathogenicity10.1099/ijs.0.65093-0
Phylogeny19060053Veillonella magna sp. nov., isolated from the jejunal mucosa of a healthy pig, and emended description of Veillonella ratti.Kraatz M, Taras DInt J Syst Evol Microbiol2008Animals, Intestinal Mucosa/*microbiology, Jejunum/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Swine/*microbiology, Veillonella/*classification/*physiology/ultrastructureGenetics10.1099/ijs.0.2008/001032-0
Pathogenicity26347298Identification of an antibacterial protein by functional screening of a human oral metagenomic library.Arivaradarajan P, Warburton PJ, Paramasamy G, Nair SP, Allan E, Mullany PFEMS Microbiol Lett2015Aldehyde Oxidoreductases/genetics, Amino Acid Sequence, Anti-Bacterial Agents/*chemistry/isolation & purification/pharmacology, Bacillus subtilis/drug effects, Bacteria/drug effects, Bacterial Proteins/*chemistry/isolation & purification/*pharmacology, Chromosomes, Artificial, Bacterial, Cloning, Molecular, Dental Plaque/*microbiology, Escherichia coli/genetics, Escherichia coli K12/drug effects, Genetic Vectors, Genomic Library, Humans, Lactobacillus casei/drug effects, *Metagenome, Molecular Sequence Data, Mutagenesis, Neisseria/*chemistry, Plasmids, Pseudomonas aeruginosa/drug effects, Saliva/*microbiology, Sequence Analysis, DNA, Staphylococcus aureus/drug effects, Staphylococcus epidermidis/drug effectsEnzymology10.1093/femsle/fnv142
Proteome28713344Outer Membrane Proteome of Veillonella parvula: A Diderm Firmicute of the Human Microbiome.Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo SFront Microbiol201710.3389/fmicb.2017.01215
29774017Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures.Wang Y, Fu L, Ren J, Yu Z, Chen T, Sun FFront Microbiol201810.3389/fmicb.2018.00872

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
956Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2008)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2008
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
44842Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 5123)https://www.ccug.se/strain?id=5123
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
86173Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264272.1StrainInfo: A central database for resolving microbial strain identifiers