Vagococcus fluvialis (DSM 5731, ATCC 49515, NCDO 2497)

Name: Vagococcus fluvialis (DSM 5731, ATCC 49515, NCDO 2497)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5262

Type strain

Strain Designation M-29c

Culture col. no. DSM 5731 ATCC 49515 NCDO 2497 CCUG 32704 CIP 102976 2 more

NCBI tax ID(s) 2738

Special Collections DSMZ CCUG CIP

History <- NCFB <- H. Hashimoto, M-29c CIP <- 1987, NCFB, Lactococcus sp. <- H. Hashimoto: strain M-29 C, Streptococcus lactis

Links

Vagococcus fluvialis M-29c is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from chicken faeces.

Gram-positive oval-shaped aerobe mesophilic human pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 5032

LMG 9464,ATCC 49515,CIP 102976,NCFB 2497,NCDO 2497,CCUG 32704,DSM 5731,NCIMB 13038,CCM 4304

@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 fluvialis

Full scientific name Vagococcus fluvialis Collins et al. 1990

BacDive ID	Other strains from **Vagococcus fluvialis** (9)	Type strain
5263	V. fluvialis M-128f, DSM 5732, NCDO 2499
5264	V. fluvialis ENDO-EH, DSM 21402
137500	V. fluvialis CIP 65.27
137806	V. fluvialis CIP 102977, DSM 18578
147041	V. fluvialis
147339	V. fluvialis CCUG 33393
150044	V. fluvialis CCUG 38909
150045	V. fluvialis CCUG 38910
150962	V. fluvialis CCUG 42871

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
119413	positive	oval-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2312	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
38745	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119413	CIP Medium 29	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2312	positive	growth	30	mesophilic
38745	positive	growth	37
51141	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
51141	aerobe
119413	facultative anaerobe
125439	obligate aerobe	96.3

Murein

@ref	Murein short key	Type
2312	A11.31	A4alpha L-Lys-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
119413	17632 ChEBI	nitrate	-	reduction
119413	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119413	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
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
119413	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
119413	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
119413	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
119413	-	-	+	+	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
119413	not determinedn.d.	+	-	-	-	+	-	-	-	-	+/-	+	+/-	+/-	-	-	-	-	+	+/-	-	+	+	+	+	+	+	+	+	-	-	+	+	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Birds	#Chicken
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2312	chicken faeces	Japan	JPN	Asia
51141	Chicken feces
119413	Animal, Chicken, feces

Taxonmaps

69479

Global distribution of 16S sequence Y18098 (>99% sequence identity) for Vagococcus fluvialis from Microbeatlas

Aquatic Samples	1703
Soil Samples	1044
Animal Samples	6217
Plant Samples	253
Total Samples	9217

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
2312			2	Risk group (German classification) According to TRBA 466
119413			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	ASM398757v1 assembly for Vagococcus fluvialis NCDO 2497	contig	GCA_003987575	2738.4	8117642867	2738	69.72
66792	ASM333731v1 assembly for Vagococcus fluvialis DSM 5731	scaffold	GCA_003337315	2738.3	2770939496	2738	69.44

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Vagococcus fluvialis strain CCUG 32704 16S-23S ribosomal RNA intergenic spacer, partial sequence	JQ697980	232	2738
20218	Vagococcus fluvialis 16S rRNA gene	Y18098	1469	2738
20218	Vagococcus fluvialis 16S ribosomal RNA	X54258	1484	2738

GC content

2312

GC-content (mol%)33.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vagococcus fluvialis DSM 5731
NCBI: GCA_003337315

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	87.30	no
125439	motility	BacteriaNetⓘ	yes	81.60	no
125439	gram_stain	BacteriaNetⓘ	positive	79.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vagococcus fluvialis DSM 5731
NCBI: GCA_003337315.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	82.49	no
125438	anaerobic	anaerobicⓘ	no	87.58	yes
125438	aerobic	aerobicⓘ	no	92.89	no
125438	spore-forming	spore-formingⓘ	no	69.46	no
125438	thermophilic	thermophileⓘ	no	94.97	yes
125438	flagellated	motile2+ⓘ	yes	58.99	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Hidden diversity in Enterococcus faecalis revealed by CRISPR2 screening: eco-evolutionary insights into a novel subspecies.	Leite VLM, Faria AR, Guerra CF, Souza SdSR, Freitas AdAR, Morais JM, Merquior VLC, Planet PJ, Teixeira LM.	Microbiol Spectr	10.1128/spectrum.01428-25	2025
	Vagococcus fluvialis isolation and sequencing from urine of healthy cattle.	Giannattasio-Ferraz S, Ene A, Maskeri L, Oliveira AP, Barbosa-Stancioli EF, Putonti C.	G3 (Bethesda)	10.1093/g3journal/jkaa034	2021
	Complete genome sequence of bile-isolated Enterococcus avium strain 352.	Yu T, Li L, Zhao Q, Wang P, Zuo X.	Gut Pathog	10.1186/s13099-019-0294-9	2019
	A Complementary Isothermal Amplification Method to the U.S. EPA Quantitative Polymerase Chain Reaction Approach for the Detection of Enterococci in Environmental Waters.	Kolm C, Martzy R, Brunner K, Mach RL, Krska R, Heinze G, Sommer R, Reischer GH, Farnleitner AH.	Environ Sci Technol	10.1021/acs.est.7b01074	2017
Phylogeny	Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA.	Heilig HG, Zoetendal EG, Vaughan EE, Marteau P, Akkermans AD, de Vos WM.	Appl Environ Microbiol	10.1128/aem.68.1.114-123.2002	2002
Enzymology	Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes.	Franks AH, Harmsen HJ, Raangs GC, Jansen GJ, Schut F, Welling GW.	Appl Environ Microbiol	10.1128/aem.64.9.3336-3345.1998	1998
	Phenotypic and genotypic characterization of Vagococcus fluvialis, including strains isolated from human sources.	Teixeira LM, Carvalho MG, Merquior VL, Steigerwalt AG, Brenner DJ, Facklam RR.	J Clin Microbiol	10.1128/jcm.35.11.2778-2781.1997	1997
Phylogeny	Identification of Enterococcus species and phenotypically similar Lactococcus and Vagococcus species by reverse checkerboard hybridization to chaperonin 60 gene sequences.	Goh SH, Facklam RR, Chang M, Hill JE, Tyrrell GJ, Burns EC, Chan D, He C, Rahim T, Shaw C, Hemmingsen SM.	J Clin Microbiol	10.1128/jcm.38.11.3953-3959.2000	2000
Phylogeny	Identification of clinically relevant enterococcus species by direct sequencing of groES and spacer region.	Tsai JC, Hsueh PR, Lin HM, Chang HJ, Ho SW, Teng LJ.	J Clin Microbiol	10.1128/jcm.43.1.235-241.2005	2005
	Lysyl-Phosphatidylglycerol: A Lipid Involved in the Resistance of Staphylococcus aureus to Antimicrobial Peptide Activity.	Vasquez A, Leidy C, Manrique-Moreno M.	Antibiotics (Basel)	10.3390/antibiotics14040349	2025
	D-Alanylcardiolipin, a major component of the unique lipid pattern of Vagococcus fluvialis.	Fischer W, Arneth-Seifert D.	J Bacteriol	10.1128/jb.180.11.2950-2957.1998	1998
Enzymology	Isolation of glucocardiolipins from Geobacillus stearothermophilus NRS 2004/3a.	Schaffer C, Beckedorf AI, Scheberl A, Zayni S, Peter-Katalinic J, Messner P.	J Bacteriol	10.1128/jb.184.23.6709-6713.2002	2002
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 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	16S ribosomal ribonucleic acid sequence analyses of lactococci and related taxa. Description of Vagococcus fluvialis gen. nov., sp. nov.	Collins MD, Ash C, Farrow JA, Wallbanks S, Williams AM	J Appl Bacteriol	10.1111/j.1365-2672.1989.tb02516.x	1989

References

#2312	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5731
#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 )
#38745	; Curators of the CIP;
#51141	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 32704
#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) .
#68371	Automatically annotated from API 50CH acid .
#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 .
#119413	Collection of Institut Pasteur ; Curators of the CIP; CIP 102976
#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 fluvialis (DSM 5731, ATCC 49515, NCDO 2497)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003987575

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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