Name: Veillonella denticariosi RBV106
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17179

Type strain:

Species: Veillonella denticariosi

Strain Designation: RBV106, RBV 106

Culture col. no.: JCM 15641, DSM 19009, CCUG 54362, CIP 109448, KCTC 15017

Strain history: CIP <- 2007, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 129.06, "Veillonella dentocariosa"

NCBI tax ID(s): 1298594 (strain), 419208 (species)

SI-ID 302971

CCUG 54362, CIP 109448, DSM 19009, JCM 15641, KCTC 15017

Special Collections

Other strains from Veillonella denticariosi

Section

Veillonella denticariosi RBV106 is an anaerobe, Gram-negative, coccus-shaped human pathogen that was isolated from human carious dentine.

coccus-shaped
Gram-negative
anaerobe
human pathogen
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Negativicutes*
	Order	*Veillonellales*
	Family	*Veillonellaceae*
	Genus	*Veillonella*
	Species	**Veillonella denticariosi**
	Full Scientific Name (LPSN)	Veillonella denticariosi Byun et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32189]	Gram stain	negative
[Ref.: #118910]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %92.109

[Ref.: #32189]	Cell shape	coccus-shaped
[Ref.: #118910]	Cell shape	coccus-shaped

[Ref.: #32189]	Motility	no
[Ref.: #118910]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.368

[Ref.: #60153]

Incubation period

2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7828]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #7828]

Culture medium growth

[Ref.: #7828]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7828]

Culture medium composition

expand / minimize

[Ref.: #7828]

Culture medium

VEILLONELLA MEDIUM (DSMZ Medium 136)

[Ref.: #7828]

Culture medium growth

[Ref.: #7828]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7828]

Culture medium composition

expand / minimize

[Ref.: #37559]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #37559]

Culture medium growth

[Ref.: #37559]

Culture medium composition

expand / minimize

[Ref.: #118910]

Culture medium

CIP Medium 20

[Ref.: #118910]

Culture medium growth

[Ref.: #118910]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7828]	growth	37 °C
[Ref.: #37559]	growth	37 °C
[Ref.: #60153]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7828]	Oxygen tolerance	anaerobe
[Ref.: #32189]	Oxygen tolerance	anaerobe
[Ref.: #60153]	Oxygen tolerance	anaerobe
[Ref.: #118910]	Oxygen tolerance	anaerobe

[Ref.: #32189]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #32189]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #32189]	lactate ChEBI	+	carbon source
[Ref.: #32189]	malate ChEBI	+	carbon source
[Ref.: #32189]	nitrate ChEBI	+	reduction
[Ref.: #118910]	nitrate ChEBI	+	reduction
[Ref.: #68380]	nitrate ChEBI	+	reduction	* from API rID32A
[Ref.: #118910]	nitrite ChEBI	-	reduction
[Ref.: #32189]	propionate ChEBI	+	carbon source
[Ref.: #32189]	pyruvate ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118910]		indole ChEBI	no
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A, API zym
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A, API zym
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A, API zym
[Ref.: #68380]	alpha-glucosidase	-	3.2.1.20	* from API rID32A, API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	-	3.2.1.23	* from API rID32A, API zym
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A, API zym
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A, API zym
[Ref.: #118910]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A, API zym
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A, API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118910]	oxidase	-
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #118910]	urease	-	3.5.1.5
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #7828]	12263	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118910]	11871	-	-	+	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7828]	Sample type/isolated from	human carious dentine
[Ref.: #7828]	Geographic location (country and/or sea, region)	Sydney
[Ref.: #7828]	Country	Australia
[Ref.: #7828]	Country ISO 3 Code	AUS
[Ref.: #7828]	Continent	Australia and Oceania

[Ref.: #60153]	Sample type/isolated from	Human carious dentin,extracted tooth
[Ref.: #60153]	Sampling date	2005-08-01
[Ref.: #60153]	Geographic location (country and/or sea, region)	NSW,Sydney
[Ref.: #60153]	Country	Australia
[Ref.: #60153]	Country ISO 3 Code	AUS
[Ref.: #60153]	Continent	Australia and Oceania

[Ref.: #67770]	Sample type/isolated from	Human carious dentine

[Ref.: #118910]	Sample type/isolated from	Human, Tooth
[Ref.: #118910]	Geographic location (country and/or sea, region)	Wentworthville
[Ref.: #118910]	Country	Australia
[Ref.: #118910]	Country ISO 3 Code	AUS
[Ref.: #118910]	Continent	Australia and Oceania
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Tooth
#Host Body-Site	#Other	#Wound

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC269263 (>99% sequence identity) for Veillonella from Microbeatlas

Aquatic Samples	1
Soil Samples	1
Animal Samples	1594
Plant Samples	4
Total Samples	1600

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7828]	Pathogenicity (human)	yes, in single cases
[Ref.: #7828]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118910]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7828]	Veillonella denticariosi strain RBV106 16S ribosomal RNA gene, partial sequence	EF185167	1497	GenBank ENA	419208 tax ID
[Ref.: #67770]	Veillonella denticariosi gene for 16S ribosomal RNA, partial sequence, strain: JCM 15641	LC269263	1414	GenBank ENA	419208 tax ID
[Ref.: #20218]	Veillonella denticariosi strain CCUG 54362 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	GQ496495	958	GenBank ENA	419208 tax ID	*
[Ref.: #20218]	Veillonella denticariosi strain CCUG 54362 clone 3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	GQ496496	719	GenBank ENA	419208 tax ID	*
[Ref.: #20218]	Veillonella denticariosi strain CCUG 54362 clone 5 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	GQ496497	1068	GenBank ENA	419208 tax ID	*
[Ref.: #20218]	Veillonella denticariosi strain CCUG 54362 clone 7 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	GQ496498	955	GenBank ENA	419208 tax ID	*
[Ref.: #20218]	Veillonella denticariosi strain CCUG 54362 clone 8 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	GQ496499	719	GenBank ENA	419208 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Veillonella denticariosi JCM 15641	GCA_001312465	contig	GenBank ENA	1298594 tax ID
[Ref.: #67770]	Veillonella denticariosi JCM 15641	GCA_002959855	contig	GenBank ENA	1298594 tax ID
[Ref.: #66792]	Veillonella denticariosi JCM 15641	1298594.3	wgs	PATRIC	1298594 tax ID	*
[Ref.: #66792]	Veillonella denticariosi JCM 15641	1298594.4	wgs	PATRIC	1298594 tax ID	*
[Ref.: #66792]	Veillonella denticariosi JCM 15641	2734481902	draft	JGI IMG/M	1298594 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Veillonella denticariosi JCM 15641 PATRIC: 1298594.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Veillonella denticariosi JCM 15641 PATRIC: 1298594.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	92.109	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	87.837	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	81.742	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	95	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.651	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90.368	yes

Availability in culture collections External links

[Ref.: #7828]

Culture collection no.

JCM 15641, DSM 19009, CCUG 54362, CIP 109448, KCTC 15017

[Ref.: #86178]

SI-ID 302971

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Veillonella denticariosi sp. nov., isolated from human carious dentine.	Byun R, Carlier JP, Jacques NA, Marchandin H, Hunter N	Int J Syst Evol Microbiol	10.1099/ijs.0.65096-0	2007	*

References

#7828

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19009

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#32189

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28431 (see below)

#37559 ; Curators of the CIP;
#60153 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54362

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68380

Automatically annotated from API rID32A .

#68382

Automatically annotated from API zym .

#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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86178

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID302971.1 )

#118910 Collection of Institut Pasteur ; Curators of the CIP; CIP 109448

#28431

IJSEM 2844 2007 ( DOI 10.1099/ijs.0.65096-0 , PubMed 18048736 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Veillonella denticariosi in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Veillonella denticariosi JCM 15641

Veillonella denticariosi JCM 15641

Change proposal

Change proposal