Name: Enterococcus rivorum S299
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132904

Type strain:

Species: Enterococcus rivorum

Strain Designation: S299

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

Strain history: <- CCM; CCM 7986 <- P. Oivanen <- R. M. Niemi; S299

NCBI tax ID(s): 762845 (species)

SI-ID 370637

LMG 25899, CCM 7986, HAMBI 3055, DSM 104544

Section

Enterococcus rivorum S299 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from pristine brook.

Gram-positive
spore-forming
mesophilic
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	*Enterococcus*
	Species	**Enterococcus rivorum**
	Full Scientific Name (LPSN)	Enterococcus rivorum Niemi et al. 2012

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %92.778

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24692]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #24692]

Culture medium growth

[Ref.: #24692]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24692]

Culture medium composition

expand / minimize

[Ref.: #24692]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #24692]

Culture medium growth

[Ref.: #24692]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24692]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #24692]			growth	30 °C

[Ref.: #24692]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %94
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.941

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68381]	alpha-cyclodextrin ChEBI	+	builds acid from	* from API rID32STR
[Ref.: #68381]	arginine ChEBI	+	hydrolysis	* from API rID32STR
[Ref.: #68381]	D-arabitol ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	D-mannitol ChEBI	+	builds acid from	* from API rID32STR
[Ref.: #68381]	D-ribose ChEBI	+	builds acid from	* from API rID32STR
[Ref.: #68381]	D-tagatose ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	glycogen ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	hippurate ChEBI	-	hydrolysis	* from API rID32STR
[Ref.: #68381]	L-arabinose ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	lactose ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	maltose ChEBI	+	builds acid from	* from API rID32STR
[Ref.: #68381]	melezitose ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	melibiose ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	methyl beta-D-glucopyranoside ChEBI	+	builds acid from	* from API rID32STR
[Ref.: #68381]	pullulan ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	raffinose ChEBI	-	builds acid from	* from API rID32STR
[Ref.: #68381]	sorbitol ChEBI	+	builds acid from	* from API rID32STR
[Ref.: #68381]	sucrose ChEBI	+	builds acid from	* from API rID32STR
[Ref.: #68381]	trehalose ChEBI	+	builds acid from	* from API rID32STR
[Ref.: #68381]	urea ChEBI	-	hydrolysis	* from API rID32STR
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68381]		acetoin ChEBI	yes	* from API rID32STR

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #68381]		acetoin ChEBI	+	* from API rID32STR

	Enzyme	Enzyme activity	EC number
[Ref.: #68381]	Alanyl-Phenylalanyl-Proline arylamidase	-		* from API rID32STR
[Ref.: #68381]	alpha-galactosidase	-	3.2.1.22	* from API rID32STR
[Ref.: #68381]	arginine dihydrolase	+	3.5.3.6	* from API rID32STR
[Ref.: #68381]	beta-galactosidase	-	3.2.1.23	* from API rID32STR
[Ref.: #68381]	beta-glucosidase	+	3.2.1.21	* from API rID32STR
[Ref.: #68381]	beta-glucuronidase	-	3.2.1.31	* from API rID32STR
[Ref.: #68381]	beta-mannosidase	+	3.2.1.25	* from API rID32STR
[Ref.: #68381]	glycyl tryptophan arylamidase	-		* from API rID32STR
[Ref.: #68381]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API rID32STR
[Ref.: #68381]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32STR
[Ref.: #68381]	urease	-	3.5.1.5	* from API rID32STR
	Only first 10 entries are displayed. Click here to see all.

API® rID32STR:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Arginine dihydrolaseADH (Arg)	beta-Glucosidasebeta GLU	beta-Galactosidasebeta GAR	beta-Glucuronidasebeta GUR	alpha-Galactosidasealpha GAL	Alkaline PhosphatasePAL	Acid from D-riboseRIB	Acid from D-mannitolMAN	Acid from sorbitolSOR	Acid from lactoseLAC	Acid from trehaloseTRE	Acid from raffinoseRAF	Acid from sucroseSAC	Acid from L-arabinoseLARA	Acid from D-arabitolDARL	Acid from alpha-cyclodextrinCDEX	Acetoin production (Voges Proskauer test)VP	Alanyl-Phenylalanyl-Proline arylamidaseAPPA	beta-Galactosidasebeta GAL	Pyrrolidonyl arylamidasePyrA	N-Acetyl-glucosaminidasebeta NAG	Glycyl-tryptophan arylamidaseGTA	Hydrolysis of hippuric acidHIP	Acid from glycogenGLYG	Acid from pullulanPUL	Acid from maltoseMAL	Acid from melibioseMEL	Acid from melezitoseMLZ	Acidification of methyl beta-D-glucopyranosideMbeta DG	Acid from D-tagatoseTAG	beta-Mannosidasebeta MAN	Urease/urea hydrolysisURE
[Ref.: #24692]	10732	+	+	-	-	-	+/-	+	+	+	-	+	-	+	-	-	+	+	-	-	-	+	-	-	-	-	+	-	-	+	-	+	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	degradation of sugar alcohols	93.75	15 of 16
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
[Ref.: #66794]	heme metabolism	21.43	3 of 14
		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.: #24692]	Sample type/isolated from	pristine brook
[Ref.: #24692]	Geographic location (country and/or sea, region)	pond Kilpilammi
[Ref.: #24692]	Country	Finland
[Ref.: #24692]	Country ISO 3 Code	FIN
[Ref.: #24692]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#River (Creek)

What are isolation sources categories?

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

[Ref.: #24692]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #24692]	Enterococcus rivorum strain S299 16S ribosomal RNA, partial sequence	NR_117043	1479	GenBank	762845 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Enterococcus rivorum LMG 25899	GCA_001742285	contig	GenBank	762845 tax ID	*
[Ref.: #66792]	Enterococcus rivorum DSM 104544	GCA_017874895	contig	GenBank	762845 tax ID	*
[Ref.: #66792]	Enterococcus rivorum strain DSM 104544	762845.5	wgs	PATRIC	762845 tax ID	*
[Ref.: #66792]	Enterococcus rivorum strain LMG 25899	762845.3	wgs	PATRIC	762845 tax ID	*
[Ref.: #66792]	Enterococcus rivorum DSM 104544	2913591362	draft	JGI IMG/M	762845 tax ID	*

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: Enterococcus rivorum strain LMG 25899 PATRIC: 762845.3
[Ref.: #69481]	spore-forming	yes	94	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Enterococcus rivorum strain DSM 104544 PATRIC: 762845.5
[Ref.: #69480]	motile	no	94.171	no
[Ref.: #69480]	flagellated	no	97.437	no
[Ref.: #69480]	gram-positive	yes	90.905	no
[Ref.: #69480]	anaerobic	no	85.555	no
[Ref.: #69480]	aerobic	no	96.075	no
[Ref.: #69480]	halophile	yes	56.563	no
[Ref.: #69480]	spore-forming	no	86.402	no
[Ref.: #69480]	glucose-util	yes	89.48	no
[Ref.: #69480]	thermophile	no	98.889	yes
[Ref.: #69480]	glucose-ferment	yes	80.438	no

Availability in culture collections External links

[Ref.: #24692]

Culture collection no.

DSM 104544, CCM 7986, HAMBI 3055, LMG 25899

[Ref.: #91182]

SI-ID 370637

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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 )

#91182

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-ID370637.1 )

* These data were automatically processed and therefore are not curated

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Search for species Enterococcus rivorum in external resources:
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Enterococcus rivorum strain LMG 25899

Enterococcus rivorum strain DSM 104544

Change proposal

Change proposal