@ref: 956
BacDive-ID: 17174
DSM-Number: 2008
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Veillonella parvula subsp. parvula Te3 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from intestinal tract.
| @ref | history |
|---|---|
| 956 | <- ATCC; ATCC 10790 <- J.E. Faber; <- A. R. Prevot; Te3 |
| 67770 | DSM 2008 <-- ATCC 10790 <-- J. E. Faber <-- A. R. Prévot Te3. |
doi: 10.13145/bacdive17174.20250331.9.3
@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
| @ref | type of hemolysis | incubation period |
|---|---|---|
| 956 | gamma | 1-2 days |
| 44842 | 2-3 days |
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 956 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | 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 |
| 956 | VEILLONELLA MEDIUM (DSMZ Medium 136) | yes | https://mediadive.dsmz.de/medium/136 | Name: 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 |
| 956 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
| @ref | growth | type | temperature |
|---|---|---|---|
| 956 | positive | growth | 37 |
| 44842 | positive | growth | 37 |
| 67770 | positive | growth | 37 |
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 956 | anaerobe | |
| 44842 | anaerobe | |
| 125439 | anaerobe | 92.3 |
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68380 | 27897 | tryptophan | - | energy source |
| 68380 | 29985 | L-glutamate | - | degradation |
| 68380 | 16199 | urea | - | hydrolysis |
| 68380 | 16024 | D-mannose | - | fermentation |
| 68380 | 17632 | nitrate | + | reduction |
| 68380 | 16634 | raffinose | - | fermentation |
| @ref | value | activity | ec |
|---|---|---|---|
| 68380 | histidine arylamidase | - | |
| 68380 | glycin arylamidase | - | |
| 68380 | alanine arylamidase | - | 3.4.11.2 |
| 68380 | glutamate decarboxylase | - | 4.1.1.15 |
| 68380 | alpha-arabinosidase | - | 3.2.1.55 |
| 68380 | beta-glucosidase | - | 3.2.1.21 |
| 68380 | beta-Galactosidase 6-phosphate | - | |
| 68380 | beta-galactosidase | - | 3.2.1.23 |
| 68380 | serine arylamidase | - | |
| 68380 | glutamyl-glutamate arylamidase | - | |
| 68380 | tyrosine arylamidase | - | |
| 68380 | leucine arylamidase | - | 3.4.11.1 |
| 68380 | phenylalanine arylamidase | - | |
| 68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
| 68380 | proline-arylamidase | - | 3.4.11.5 |
| 68380 | L-arginine arylamidase | - | |
| 68380 | alkaline phosphatase | - | 3.1.3.1 |
| 68380 | tryptophan deaminase | - | 4.1.99.1 |
| 68380 | alpha-fucosidase | - | 3.2.1.51 |
| 68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
| 68380 | beta-glucuronidase | - | 3.2.1.31 |
| 68380 | alpha-glucosidase | - | 3.2.1.20 |
| 68380 | alpha-galactosidase | - | 3.2.1.22 |
| 68380 | urease | - | 3.5.1.5 |
| @ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 956 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - |
| 956 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - |
| 956 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| 956 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
| @ref | sample type |
|---|---|
| 956 | intestinal tract |
| 44842 | Intestinal tract |
| 67770 | Intestinal tract |
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Veillonella parvula gene for 16S ribosomal RNA, partial sequence, strain: JCM 12972 | AB538437 | 1524 | nuccore | 29466 |
| 20218 | Veillonella parvula strain ATCC 10790 16S ribosomal RNA gene, partial sequence | AY995767 | 1497 | nuccore | 479436 |
| 20218 | Veillonella parvula DSM 2008 16S ribosomal RNA gene, partial sequence | HM007566 | 1345 | nuccore | 479436 |
| 20218 | V.parvula 16S rRNA gene | X84005 | 1513 | nuccore | 479436 |
| 124043 | Veillonella parvula DSM 2008 gene for 16S rRNA, partial sequence. | LC752359 | 588 | nuccore | 479436 |
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Veillonella parvula NCTC11810 | GCA_900186885 | complete | ncbi | 29466 |
| 66792 | Veillonella parvula DSM 2008 | GCA_000024945 | complete | ncbi | 479436 |
| 66792 | Veillonella parvula DSM 2008 | 479436.6 | complete | patric | 479436 |
| 66792 | Veillonella parvula strain NCTC11810 | 29466.62 | complete | patric | 29466 |
| 66792 | Veillonella parvula Te3, DSM 2008 | 646311965 | complete | img | 479436 |
| 66792 | Veillonella parvula NCTC 11810 | 2814123216 | complete | img | 29466 |
| @ref | GC-content | method |
|---|---|---|
| 956 | 38.0 | |
| 67770 | 38 | thermal denaturation, midpoint method (Tm) |
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 90.189 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 81.097 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 88.212 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 77.42 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 94.293 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 87.63 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 79.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 64.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 89.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 92.3 |
@ref: 956
culture collection no.: CCUG 5123, ATCC 17742, DSM 2008, ATCC 10790, JCM 12972, NCTC 11810
| topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 1775087 | Biological effects of Veillonella parvula and Bacteroides intermedius lipopolysaccharides. | Matera G, Liberto MC, Berlinghieri MC, Foca A | Microbiologica | 1991 | Animals, *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, *Veillonella | Pathogenicity | |
| Lipids | 7056696 | Effects of growth temperature on fatty acid and alk-1-enyl group compositions of Veillonella parvula and Megasphaera elsdenii phospholipids. | Johnston NC, Goldfine H | J Bacteriol | 1982 | Fatty Acids/analysis, Membrane Lipids/analysis, Phosphatidylethanolamines/analysis, Phosphatidylserines/analysis, Phospholipids/*analysis, Plasmalogens/*analysis, Temperature, Veillonella/*analysis/growth & development, Veillonellaceae/*analysis/growth & development | 10.1128/jb.149.2.567-575.1982 | |
| Enzymology | 7251145 | Identification of a Streptococcus salivarius cell wall component mediating coaggregation with Veillonella alcalescens V1. | Weerkamp AH, McBride BC | Infect Immun | 1981 | Bacterial Proteins/*physiology, Cell Wall/analysis, Electrophoresis, Polyacrylamide Gel, Glycoproteins/*physiology, Immunoelectrophoresis, Isoelectric Focusing, Streptococcus/*analysis/physiology/ultrastructure, Veillonella/*physiology | 10.1128/iai.32.2.723-730.1981 | |
| Phylogeny | 18319459 | Veillonella 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 D | Int J Syst Evol Microbiol | 2008 | Anaerobiosis, 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/physiology | Pathogenicity | 10.1099/ijs.0.65093-0 |
| Phylogeny | 19060053 | Veillonella magna sp. nov., isolated from the jejunal mucosa of a healthy pig, and emended description of Veillonella ratti. | Kraatz M, Taras D | Int J Syst Evol Microbiol | 2008 | Animals, Intestinal Mucosa/*microbiology, Jejunum/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Swine/*microbiology, Veillonella/*classification/*physiology/ultrastructure | Genetics | 10.1099/ijs.0.2008/001032-0 |
| Pathogenicity | 26347298 | Identification of an antibacterial protein by functional screening of a human oral metagenomic library. | Arivaradarajan P, Warburton PJ, Paramasamy G, Nair SP, Allan E, Mullany P | FEMS Microbiol Lett | 2015 | Aldehyde 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 effects | Enzymology | 10.1093/femsle/fnv142 |
| Proteome | 28713344 | Outer 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 S | Front Microbiol | 2017 | 10.3389/fmicb.2017.01215 | ||
| 29774017 | Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures. | Wang Y, Fu L, Ren J, Yu Z, Chen T, Sun F | Front Microbiol | 2018 | 10.3389/fmicb.2018.00872 |
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 956 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2008) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2008 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 44842 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 5123) | https://www.ccug.se/strain?id=5123 | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 68380 | Automatically annotated from API rID32A | |||||
| 69479 | João 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 | |||
| 86173 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID264272.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | ||||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |
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