Enterococcus rivorum (DSM 104544, CCM 7986, HAMBI 3055)

Name: Enterococcus rivorum (DSM 104544, CCM 7986, HAMBI 3055)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132904

Type strain

Strain Designation S299

Culture col. no. DSM 104544 CCM 7986 HAMBI 3055 LMG 25899 S299

NCBI tax ID(s) 762845

Special Collections DSMZ

History <- CCM; CCM 7986 <- P. Oivanen <- R. M. Niemi; S299

Links

Enterococcus rivorum S299 is a bacterium that was isolated from pristine brook.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 370637

LMG 25899,CCM 7986,HAMBI 3055,DSM 104544

@ref 20215

Last LPSN update 2026-02-09 11:31:49

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Enterococcaceae

Genus Enterococcus

Species Enterococcus rivorum

Full scientific name Enterococcus rivorum Niemi et al. 2012

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24692	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
24692	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)
24692	positive	growth	30

Physiology and metabolism

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68381	40585 ChEBI	alpha-cyclodextrin	+	builds acid from	from API rID32STR
68381	29016 ChEBI	arginine	+	hydrolysis	from API rID32STR
68381	18333 ChEBI	D-arabitol	-	builds acid from	from API rID32STR
68381	16899 ChEBI	D-mannitol	+	builds acid from	from API rID32STR
68381	16988 ChEBI	D-ribose	+	builds acid from	from API rID32STR
68381	16443 ChEBI	D-tagatose	-	builds acid from	from API rID32STR
68381	28087 ChEBI	glycogen	-	builds acid from	from API rID32STR
68381	606565 ChEBI	hippurate	-	hydrolysis	from API rID32STR
68381	30849 ChEBI	L-arabinose	-	builds acid from	from API rID32STR
68381	17716 ChEBI	lactose	-	builds acid from	from API rID32STR
68381	17306 ChEBI	maltose	+	builds acid from	from API rID32STR
68381	6731 ChEBI	melezitose	-	builds acid from	from API rID32STR
68381	28053 ChEBI	melibiose	-	builds acid from	from API rID32STR
68381	320055 ChEBI	methyl beta-D-glucopyranoside	+	builds acid from	from API rID32STR
68381	27941 ChEBI	pullulan	-	builds acid from	from API rID32STR
68381	16634 ChEBI	raffinose	-	builds acid from	from API rID32STR
68381	30911 ChEBI	sorbitol	+	builds acid from	from API rID32STR
68381	17992 ChEBI	sucrose	+	builds acid from	from API rID32STR
68381	27082 ChEBI	trehalose	+	builds acid from	from API rID32STR
68381	16199 ChEBI	urea	-	hydrolysis	from API rID32STR

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68381	15688 ChEBI	acetoin		from API rID32STR

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
68381	15688 ChEBI	acetoin	+	from API rID32STR

Enzymes

@ref	Value	Activity	Ec
68381	Alanyl-Phenylalanyl-Proline arylamidase	-		from API rID32STR
68381	alpha-galactosidase	-	3.2.1.22	from API rID32STR
68381	arginine dihydrolase	+	3.5.3.6	from API rID32STR
68381	beta-galactosidase	-	3.2.1.23	from API rID32STR
68381	beta-glucosidase	+	3.2.1.21	from API rID32STR
68381	beta-glucuronidase	-	3.2.1.31	from API rID32STR
68381	beta-mannosidase	+	3.2.1.25	from API rID32STR
68381	glycyl tryptophan arylamidase	-		from API rID32STR
68381	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32STR
68381	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32STR
68381	urease	-	3.5.1.5	from API rID32STR

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	vitamin K metabolism	100	5 of 5
66794	aspartate and asparagine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	degradation of sugar alcohols	93.75	15 of 16
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	purine metabolism	84.04	79 of 94
66794	pyrimidine metabolism	82.22	37 of 45
66794	starch degradation	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	histidine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	Entner Doudoroff pathway	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	citric acid cycle	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	oxidative phosphorylation	61.54	56 of 91
66794	flavin biosynthesis	60	9 of 15
66794	glycine betaine biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	metabolism of disaccharids	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	glutamate and glutamine metabolism	53.57	15 of 28
66794	degradation of pentoses	53.57	15 of 28
66794	lipid metabolism	51.61	16 of 31
66794	ethanol fermentation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	butanoate fermentation	50	2 of 4
66794	lysine metabolism	50	21 of 42
66794	ribulose monophosphate pathway	50	1 of 2
66794	tryptophan metabolism	47.37	18 of 38
66794	urea cycle	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	allantoin degradation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	propionate fermentation	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	ascorbate metabolism	31.82	7 of 22
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	vitamin B12 metabolism	26.47	9 of 34
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23
66794	heme metabolism	21.43	3 of 14

API rID32STR

@ref	ADH (Arg)	beta GLU	beta GAR	beta GUR	alpha GAL	PAL	RIB	MAN	SOR	LAC	TRE	RAF	SAC	LARA	DARL	Acid from alpha-cyclodextrinCDEX	Acetoin production (Voges Proskauer test)VP	Alanyl-Phenylalanyl-Proline arylamidaseAPPA	beta GAL	Pyrrolidonyl arylamidasePyrA	N-Acetyl-glucosaminidasebeta NAG	Glycyl-tryptophan arylamidaseGTA	HIP	GLYG	PUL	MAL	MEL	MLZ	Acidification of methyl beta-D-glucopyranosideMbeta DG	TAG	beta MAN	URE
24692	+	+	-	-	-	+/-	+	+	+	-	+	-	+	-	-	+	+	-	-	-	+	-	-	-	-	+	-	-	+	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24692	pristine brook	pond Kilpilammi	Finland	FIN	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24692	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4264830v1 assembly for Enterococcus rivorum CCM 7986	contig	GCA_042648305			762845	72.41
66792	ASM1787489v1 assembly for Enterococcus rivorum DSM 104544	contig	GCA_017874895	762845.5	2913591362	762845	60.46
66792	ASM174228v1 assembly for Enterococcus rivorum LMG 25899	contig	GCA_001742285	762845.3	8032314035	762845	60.17
124043	ASM4268382v1 assembly for Enterococcus rivorum CCM 7986	contig	GCA_042683825			762845	32.43

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
24692	Enterococcus rivorum strain S299 16S ribosomal RNA, partial sequence	NR_117043	1479	762845
124043	Enterococcus rivorum partial 16S rRNA gene, type strain HAMBI 3055T	FN822765	1479	762845
124043	Enterococcus rivorum strain CCM 7986 16S ribosomal RNA gene, partial sequence.	MT760194	1401	762845

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Enterococcus rivorum LMG 25899
NCBI: GCA_001742285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	74.00	no
125439	motility	BacteriaNetⓘ	yes	67.30	no
125439	gram_stain	BacteriaNetⓘ	variable	70.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	83.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Enterococcus rivorum strain DSM 104544
PATRIC: 762845.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	84.61	no
125438	anaerobic	anaerobicⓘ	no	85.15	no
125438	aerobic	aerobicⓘ	no	94.15	no
125438	spore-forming	spore-formingⓘ	no	72.36	no
125438	thermophilic	thermophileⓘ	no	93.49	yes
125438	flagellated	motile2+ⓘ	no	88.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Systematically investigating and identifying bacteriocins in the human gut microbiome.	Zhang D, Zou Y, Shi Y, Zhang J, Liu J, Wu G, Zhang J, Gao Y, Chen M, Li YX.	Cell Genom	10.1016/j.xgen.2025.100983	2025
	A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome.	Zhang D, Zhang J, Kalimuthu S, Liu J, Song ZM, He BB, Cai P, Zhong Z, Feng C, Neelakantan P, Li YX.	Microbiome	10.1186/s40168-023-01540-y	2023
Phylogeny	Enterococcus rivorum sp. nov., from water of pristine brooks.	Niemi RM, Ollinkangas T, Paulin L, Svec P, Vandamme P, Karkman A, Kosina M, Lindstrom K	Int J Syst Evol Microbiol	10.1099/ijs.0.038257-0	2011

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 )
#24692	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104544
#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 )
#68381	Automatically annotated from API rID32STR .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Enterococcus rivorum (DSM 104544, CCM 7986, HAMBI 3055)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32STR

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042648305

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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