Name: Vagococcus penaei CD276
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133543

Type strain:

Species: Vagococcus penaei

Strain Designation: CD276, CD 276

Culture col. no.: LMG 24833, CIP 109914, CCM 8416

Strain history: CIP <- 2008, E. Jaffrès, INRA, Nantes, France: strain CD 276

NCBI tax ID(s): 633807 (species)

SI-ID 360632

LMG 24833, CIP 109914, CCM 8416, CCUG 73526

Section

Vagococcus penaei CD276 is a facultative anaerobe, Gram-positive, coccus-shaped bacterium that was isolated from Shelled shrimp cook.

coccus-shaped
Gram-positive
facultative anaerobe
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	*Bacilli*
	Order	*Lactobacillales*
	Family	*Enterococcaceae*
	Genus	*Vagococcus*
	Species	**Vagococcus penaei**
	Full Scientific Name (LPSN)	Vagococcus penaei Jaffrès et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29425]	Gram stain	positive
[Ref.: #121657]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29425]	Cell width	0.5-1 µm

[Ref.: #29425]	Cell shape	coccus-shaped
[Ref.: #121657]	Cell shape	oval-shaped

[Ref.: #29425]	Motility	no
[Ref.: #121657]	Motility	yes

[Ref.: #29425]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37693]

Culture medium

MEDIUM 29- Brain heart agar

[Ref.: #37693]

Culture medium growth

[Ref.: #37693]

Culture medium composition

expand / minimize

[Ref.: #121657]

Culture medium

CIP Medium 29

[Ref.: #121657]

Culture medium growth

[Ref.: #121657]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #29425]	growth	10-30 °C
[Ref.: #29425]	optimum	30 °C
[Ref.: #37693]	growth	30 °C

[Ref.: #29425]	Temperature range	mesophilic
[Ref.: #37693]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29425]			optimum	7
[Ref.: #29425]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29425]	Oxygen tolerance	facultative anaerobe
[Ref.: #121657]	Oxygen tolerance	facultative anaerobe

[Ref.: #29425]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %90
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.902

[Ref.: #29425]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29425]	maltose ChEBI	+	carbon source
[Ref.: #121657]	nitrate ChEBI	-	reduction
[Ref.: #121657]	nitrite ChEBI	-	reduction
[Ref.: #29425]	raffinose ChEBI	+	carbon source
[Ref.: #29425]	ribose ChEBI	+	carbon source
[Ref.: #29425]	sucrose ChEBI	+	carbon source
[Ref.: #29425]	trehalose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #121657]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #29425]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121657]	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.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121657]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121657]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #121657]	12214	-	+	+	+	-	+	-	+	-	+	+	+	-	+	-	+	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	flavin biosynthesis	53.33	8 of 15
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	leucine metabolism	38.46	5 of 13
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	histidine metabolism	31.03	9 of 29
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #121657]	Sample type/isolated from	Shelled shrimp cook
[Ref.: #121657]	Geographic location (country and/or sea, region)	Nantes
[Ref.: #121657]	Country	France
[Ref.: #121657]	Country ISO 3 Code	FRA
[Ref.: #121657]	Continent	Europe
[Ref.: #121657]	Isolation date	2006
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence FJ360897 (>99% sequence identity) for Vagococcus penaei from Microbeatlas

Aquatic Samples	74
Soil Samples	25
Animal Samples	863
Plant Samples	63
Total Samples	1025

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

[Ref.: #121657]

Biosafety level

Risk group (French classification)

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #29425]	Vagococcus penaei strain CD 276 16S ribosomal RNA gene, complete sequence	FJ360897	1550	GenBank	633807 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Vagococcus penaei LMG 24833	GCA_003987515	contig	GenBank	633807 tax ID	*
[Ref.: #66792]	Vagococcus penaei CD276T	GCA_001998885	complete	GenBank	633807 tax ID	*
[Ref.: #66792]	Vagococcus penaei strain CD276	633807.3	complete	PATRIC	633807 tax ID	*
[Ref.: #66792]	Vagococcus penaei strain LMG 24833	633807.5	wgs	PATRIC	633807 tax ID	*
[Ref.: #66792]	Vagococcus penaei LMG 24833	2894095031	draft	JGI IMG/M	633807 tax ID	*

[Ref.: #29425]

GC-content

35.4 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Vagococcus penaei CD276 NCBI: GCA_001998885.1
[Ref.: #69481]	spore-forming	no	90	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Vagococcus penaei CD276 NCBI: GCA_001998885.1
[Ref.: #69480]	flagellated	no	86.032	yes
[Ref.: #69480]	gram-positive	yes	86.262	yes
[Ref.: #69480]	anaerobic	no	93.562	yes
[Ref.: #69480]	halophile	yes	74.525	no
[Ref.: #69480]	spore-forming	no	76.857	no
[Ref.: #69480]	glucose-util	yes	88.592	no
[Ref.: #69480]	aerobic	no	94.012	yes
[Ref.: #69480]	thermophile	no	98.034	yes
[Ref.: #69480]	motile	no	61.888	yes
[Ref.: #69480]	glucose-ferment	yes	83.713	no

Availability in culture collections External links

[Ref.: #29425]

Culture collection no.

LMG 24833, CIP 109914, CCM 8416

[Ref.: #91496]

SI-ID 360632

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vagococcus teuberi sp. nov., isolated from the Malian artisanal sour milk fene.	Wullschleger S, Jans C, Seifert C, Baumgartner S, Lacroix C, Bonfoh B, Stevens MJA, Meile L	Syst Appl Microbiol	10.1016/j.syapm.2017.11.003	2017	*
Phylogeny	Vagococcus acidifermentans sp. nov., isolated from an acidogenic fermentation bioreactor.	Wang L, Cui YS, Kwon CS, Lee ST, Lee JS, Im WT	Int J Syst Evol Microbiol	10.1099/ijs.0.022087-0	2010	*
Phylogeny	Vagococcus penaei sp. nov., isolated from spoilage microbiota of cooked shrimp (Penaeus vannamei).	Jaffres E, Prevost H, Rossero A, Joffraud JJ, Dousset X	Int J Syst Evol Microbiol	10.1099/ijs.0.012872-0	2009	*
Phylogeny	Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula.	Tak EJ, Kim HS, Lee JY, Kang W, Hyun DW, Kim PS, Shin NR, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002131	2017	*

References

#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 )

#29425

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 #25831 (see below)

#37693 ; Curators of the CIP;

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#91496

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-ID360632.1 )

#121657 Collection of Institut Pasteur ; Curators of the CIP; CIP 109914

#25831

IJSEM 2159 2010 ( DOI 10.1099/ijs.0.012872-0 , PubMed 19897618 )

* These data were automatically processed and therefore are not curated

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