Vagococcus elongatus (DSM 21480, CCUG 51432, NRRL B-41357)

Name: Vagococcus elongatus (DSM 21480, CCUG 51432, NRRL B-41357)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5268

Type strain

Strain Designation PPC9

Culture col. no. DSM 21480 CCUG 51432 NRRL B-41357 CIP 109559 PPC9 1 more

NCBI tax ID(s) 180344

Special Collections DSMZ CCUG CIP Literature strains

History <- CCUG <- T. R. Whitehead, USDA, Peoria, IL, USA; PPC9 CIP <- CCUG 2007 <- 2005, T. Whitehead, USDA, Peoria, IL, USA: strain PPC9

Links

Vagococcus elongatus PPC9 is a microaerophile, mesophilic, Gram-positive prokaryote that was isolated from swine-manure storage pit.

Gram-positive coccus-shaped microaerophile mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 296138

NRRL B-41357,CCUG 51432,CIP 109559,CCM 8415,DSM 21480

@ref 20215

Last LPSN update 2026-02-09 11:18:55

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Enterococcaceae

Genus Vagococcus

Species Vagococcus elongatus

Full scientific name Vagococcus elongatus Lawson et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
31968	positive	coccus-shaped
119019	positive	coccus-shaped

Pigmentation

31968

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15731	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
37767	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119019	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15731	positive	growth	37	mesophilic
31968	positive	optimum	37	mesophilic
37767	positive	growth	37	mesophilic
59187	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
15731	microaerophile
15731	aerobe
31968	anaerobe
59187	microaerophile

Spore formation

31968

Spore formationno

Observation

31968

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
31968	4853 ChEBI	esculin	+	hydrolysis
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
119019	17632 ChEBI	nitrate	-	reduction
119019	16301 ChEBI	nitrite	-	reduction
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
119019	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
31968	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	-	3.2.1.23	from API zym
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	+	3.2.1.21	from API zym
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
119019	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
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68382	leucine arylamidase	+	3.4.11.1	from API zym
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119019	oxidase	-
68380	phenylalanine arylamidase	+		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	+		from API rID32A
119019	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	aspartate and asparagine metabolism	100	9 of 9
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	pentose phosphate pathway	100	11 of 11
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	starch degradation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	purine metabolism	79.79	75 of 94
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	degradation of sugar alcohols	75	12 of 16
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	acetoin degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	vitamin B6 metabolism	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	methionine metabolism	61.54	16 of 26
66794	vitamin B1 metabolism	61.54	8 of 13
66794	leucine metabolism	61.54	8 of 13
66794	NAD metabolism	61.11	11 of 18
66794	oxidative phosphorylation	60.44	55 of 91
66794	hydrogen production	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	non-pathway related	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	sulfopterin metabolism	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	degradation of pentoses	50	14 of 28
66794	suberin monomers biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	tryptophan metabolism	47.37	18 of 38
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	proline metabolism	45.45	5 of 11
66794	lysine metabolism	45.24	19 of 42
66794	degradation of hexoses	44.44	8 of 18
66794	citric acid cycle	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	lipoate biosynthesis	40	2 of 5
66794	methylglyoxal degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	degradation of sugar acids	36	9 of 25
66794	tyrosine metabolism	35.71	5 of 14
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	octane oxidation	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	enterobactin biosynthesis	33.33	1 of 3
66794	flavin biosynthesis	33.33	5 of 15
66794	sphingosine metabolism	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	lipid metabolism	32.26	10 of 31
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	androgen and estrogen metabolism	25	4 of 16
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	biotin biosynthesis	25	1 of 4
66794	molybdenum cofactor biosynthesis	22.22	2 of 9
66794	nitrate assimilation	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
119019	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	+	-	-	-

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
15731	-	-	+	-	-	+	+	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	#Container (Reservoir)
#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
15731	swine-manure storage pit		Peoria	USA	USA	North America
59187	Stored swine manure	1998	IL,Peoria	USA	USA	North America
119019	Stored swine manure		Peoria, Illinois	United States of America	USA	North America	1998

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15731	1	Risk group (German classification) According to TRBA 466
119019	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM398764v1 assembly for Vagococcus elongatus CCUG 51432	contig	GCA_003987645	180344.3	2894097338	180344	63.68

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15731	UNVERIFIED_ORG: Vagococcus elongatus strain PPC9 16S ribosomal RNA gene, partial sequence	AF445297	1554		180344

GC content

15731

GC-content (mol%)44.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vagococcus elongatus CCUG 51432
NCBI: GCA_003987645

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	79.40	no
125439	motility	BacteriaNetⓘ	yes	79.10	no
125439	gram_stain	BacteriaNetⓘ	variable	80.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vagococcus elongatus strain CCUG 51432
PATRIC: 180344.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.20	yes
125438	anaerobic	anaerobicⓘ	no	79.31	no
125438	spore-forming	spore-formingⓘ	no	69.97	no
125438	aerobic	aerobicⓘ	no	93.38	no
125438	thermophilic	thermophileⓘ	no	94.00	no
125438	flagellated	motile2+ⓘ	no	87.98	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vagococcus zengguangii sp. nov., isolated from yak faeces.	Ge Y, Jin D, Lai XH, Yang J, Lu S, Huang Y, Zheng H, Zhang X, Xu J	J Microbiol	10.1007/s12275-021-0406-3	2020
Phylogeny	Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content.	Ge Y, Yang J, Lai XH, Zhang G, Jin D, Lu S, Wang B, Huang Y, Huang Y, Ren Z, Zhang X, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004061	2020
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 elongatus sp. nov., isolated from a swine-manure storage pit.	Lawson PA, Falsen E, Cotta MA, Whitehead TR	Int J Syst Evol Microbiol	10.1099/ijs.0.64730-0	2007

References

#15731	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21480
#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 )
#28223	IJSEM 751 2007 ( DOI 10.1099/ijs.0.64730-0 , PubMed 17392200 )
#31968	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 #28223
#37767	; Curators of the CIP;
#59187	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 51432
#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 )
#68380	Automatically annotated from API rID32A .
#68382	Automatically annotated from API zym .
#119019	Collection of Institut Pasteur ; Curators of the CIP; CIP 109559
#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 )

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Vagococcus elongatus (DSM 21480, CCUG 51432, NRRL B-41357)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003987645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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