Vagococcus penaei (LMG 24833, CIP 109914, CD276)

Name: Vagococcus penaei (LMG 24833, CIP 109914, CD276)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133543

Type strain

Strain Designation CD276, CD 276

Culture col. no. LMG 24833 CIP 109914 CD276 CCM 8416 CD 276

NCBI tax ID(s) 633807

Special Collections CIP Literature strains

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

Links

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

Gram-positive coccus-shaped facultative anaerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 360632

LMG 24833,CIP 109914,CCM 8416,CCUG 73526

@ref 20215

Last LPSN update 2026-02-09 11:31:58

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Enterococcaceae

Genus Vagococcus

Species Vagococcus penaei

Full scientific name Vagococcus penaei Jaffrès et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Motility
29425	positive	0.5-1 µm	coccus-shaped
121657	positive		oval-shaped

Pigmentation

29425

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
37693	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
121657	CIP Medium 29			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
29425	positive	growth	10-30
29425	positive	optimum	30	mesophilic
37693	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
29425	positive	optimum	7
29425	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29425	facultative anaerobe
121657	facultative anaerobe
125439	microaerophile	92.6

Spore formation

29425

Spore formationno

Observation

29425

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29425	17306 ChEBI	maltose	+	carbon source
121657	17632 ChEBI	nitrate	-	reduction
121657	16301 ChEBI	nitrite	-	reduction
29425	16634 ChEBI	raffinose	+	carbon source
29425	33942 ChEBI	ribose	+	carbon source
29425	17992 ChEBI	sucrose	+	carbon source
29425	27082 ChEBI	trehalose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121657	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
29425	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121657	catalase	-	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121657	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
121657	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

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

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121657	-	+	+	+	-	+	-	+	-	+	+	+	-	+	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
121657	Shelled shrimp cook	Nantes	France	FRA	Europe	2006

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
121657	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM199888v1 assembly for Vagococcus penaei CD276	complete	GCA_001998885	633807.3	2987189949	633807	95.91
66792	ASM398751v1 assembly for Vagococcus penaei LMG 24833	contig	GCA_003987515	633807.5	2894095031	633807	66.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29425	Vagococcus penaei strain CD 276 16S ribosomal RNA gene, complete sequence	FJ360897	1550		633807

GC content

29425

GC-content (mol%)35.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vagococcus penaei strain CD276
PATRIC: 633807.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	53.50	no
125439	motility	BacteriaNetⓘ	no	52.60	no
125439	gram_stain	BacteriaNetⓘ	positive	84.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	92.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vagococcus penaei CD276
NCBI: GCA_001998885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.15	yes
125438	anaerobic	anaerobicⓘ	no	87.72	yes
125438	aerobic	aerobicⓘ	no	96.33	yes
125438	spore-forming	spore-formingⓘ	no	71.88	yes
125438	thermophilic	thermophileⓘ	no	95.68	yes
125438	flagellated	motile2+ⓘ	yes	56.83	no

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 )
#25831	IJSEM 2159 2010 ( DOI 10.1099/ijs.0.012872-0 , PubMed 19897618 )
#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
#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 .
#121657	Collection of Institut Pasteur ; Curators of the CIP; CIP 109914
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Vagococcus penaei (LMG 24833, CIP 109914, CD276)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001998885

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media