Name: Ruegeria denitrificans 5OM10
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 135100

Type strain:

Species: Ruegeria denitrificans

Strain Designation: 5OM10

Culture col. no.: CIP 108403, CECT 5091, LMG 29896

Strain history: CIP <- 2004, M.J. Pujalte, Burjasot, Spain: strain 5OM10

NCBI tax ID(s): 1715692 (species)

Section

Ruegeria denitrificans 5OM10 is an aerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies.

coccus-shaped
colony-forming
Gram-negative
aerobe
chemoorganotroph
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Ruegeria*
	Species	**Ruegeria denitrificans**
	Full Scientific Name (LPSN)	Ruegeria denitrificans Arahal et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66611]	Gram stain	negative
[Ref.: #33961]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #66611]	Cell shape	coccus-shaped
[Ref.: #33961]	Cell shape	rod-shaped

[Ref.: #66611]	Motility	no
[Ref.: #33961]	Motility	yes

[Ref.: #66611]	Colony shape	circular
[Ref.: #66611]	Cultivation medium used	Marine agar (MA)

[Ref.: #66611]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #33961]

Culture medium

Marine agar (MA)

[Ref.: #33961]

Culture medium growth

[Ref.: #33961]

Culture medium composition

expand / minimize

[Ref.: #66611]

Culture medium

Marine agar (MA)

[Ref.: #66611]

Culture medium growth

[Ref.: #33961]

Culture medium

CIP Medium 13

[Ref.: #33961]

Culture medium growth

[Ref.: #33961]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #33961]		growth	25 °C
[Ref.: #33961]	no	growth	41 °C
[Ref.: #33961]	no	growth	37 °C
[Ref.: #33961]	no	growth	5 °C
[Ref.: #33961]		growth	15-30 °C
[Ref.: #33961]	no	growth	45 °C
[Ref.: #66611]	no	growth	37 °C
[Ref.: #66611]		optimum	26 °C
[Ref.: #66611]		optimum	15 °C
[Ref.: #66611]	no	growth	4 °C

[Ref.: #33961]	Temperature range	mesophilic
[Ref.: #33961]	Temperature range	thermophilic
[Ref.: #33961]	Temperature range	mesophilic
[Ref.: #33961]	Temperature range	psychrophilic
[Ref.: #33961]	Temperature range	thermophilic
[Ref.: #66611]	Temperature range	mesophilic
[Ref.: #66611]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #66611]			optimum	7
[Ref.: #66611]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66611]

Oxygen tolerance

aerobe

[Ref.: #66611]

Nutrition type

chemoorganotroph

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Salt	Tested relation		Salt conc.
[Ref.: #66611]	Marine salts		growth	1.5-6	%
[Ref.: #33961]	NaCl	no	growth	8	%
[Ref.: #33961]	NaCl	no	growth	6	%
[Ref.: #33961]	NaCl	no	growth	4	%
[Ref.: #33961]	NaCl	no	growth	2	%
[Ref.: #33961]	NaCl	no	growth	0	%
[Ref.: #66611]	NaCl	no	growth	7	%
[Ref.: #66611]	Marine salts	no	growth	1	%
[Ref.: #66611]	Marine salts		optimum	3	%
[Ref.: #33961]	NaCl	no	growth	10	%

[Ref.: #66611]	Observation	Cells do not accumulate PHB.
[Ref.: #66611]	Observation	unable to ferment carbohydrates
[Ref.: #66611]	Observation	No growth without added salts; sodium and magnesium ions are required for growth.
[Ref.: #66611]	Observation	Bacteriochlorophyll a is not produced, puf genes are absent.
[Ref.: #66611]	Observation	Carbon monoxide oxidation genes are present.
[Ref.: #66611]	Observation	Genes for cyanophycin synthesis and degradation (cyanophycin synthase, cyanophycinase and isoaspartyl dipeptidase) are also present.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66611]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #66611]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #66611]	4-aminobutyrate ChEBI	+	carbon source
[Ref.: #66611]	4-nitrophenyl beta-D-glucopyranoside ChEBI	+	hydrolysis
[Ref.: #66611]	amygdalin ChEBI	-	growth
[Ref.: #66611]	butyrate ChEBI	+	carbon source
[Ref.: #66611]	casein	+	hydrolysis
[Ref.: #66611]	cellobiose ChEBI	-	growth
[Ref.: #33961]	citrate ChEBI	-	carbon source
[Ref.: #66611]	D-fructose ChEBI	+/-	growth
[Ref.: #66611]	D-galactose ChEBI	+	carbon source
[Ref.: #66611]	D-galacturonic acid ChEBI	-	growth
[Ref.: #66611]	D-glucarate ChEBI	-	growth
[Ref.: #66611]	D-gluconate ChEBI	-	growth
[Ref.: #66611]	D-glucose ChEBI	+	carbon source
[Ref.: #66611]	D-glucuronate ChEBI	-	growth
[Ref.: #66611]	D-glycerate ChEBI	+	carbon source
[Ref.: #66611]	D-mannitol ChEBI	+	carbon source
[Ref.: #66611]	D-mannose ChEBI	+	carbon source
[Ref.: #66611]	D-ribose ChEBI	+	carbon source
[Ref.: #66611]	D-sorbitol ChEBI	+	carbon source
[Ref.: #66611]	D-xylose ChEBI	-	growth
[Ref.: #66611]	dna ChEBI	+	hydrolysis
[Ref.: #66611]	esculin ChEBI	+	hydrolysis
[Ref.: #33961]	esculin ChEBI	-	hydrolysis
[Ref.: #66611]	gelatin ChEBI	+	hydrolysis
[Ref.: #33961]	glucose ChEBI	+/-	degradation
[Ref.: #66611]	glycerol ChEBI	+	carbon source
[Ref.: #66611]	glycine ChEBI	+/-	growth
[Ref.: #33961]	hippurate ChEBI	-	hydrolysis
[Ref.: #66611]	L-alanine ChEBI	+	carbon source
[Ref.: #66611]	L-arabinose ChEBI	-	growth
[Ref.: #66611]	L-arginine ChEBI	+	carbon source
[Ref.: #66611]	L-aspartate ChEBI	+	carbon source
[Ref.: #66611]	L-citrulline ChEBI	+	carbon source
[Ref.: #66611]	L-glutamate ChEBI	+	carbon source
[Ref.: #66611]	L-histidine ChEBI	-	growth
[Ref.: #66611]	L-leucine ChEBI	+	carbon source
[Ref.: #66611]	L-lysine ChEBI	+	carbon source
[Ref.: #66611]	L-ornithine ChEBI	+	carbon source
[Ref.: #66611]	L-rhamnose ChEBI	+	carbon source
[Ref.: #66611]	L-serine ChEBI	+	carbon source
[Ref.: #66611]	L-threonine ChEBI	+	carbon source
[Ref.: #66611]	L-tyrosine ChEBI	+	carbon source
[Ref.: #66611]	lactose ChEBI	-	growth
[Ref.: #66611]	malate ChEBI	+	carbon source
[Ref.: #33961]	malonate ChEBI	-	assimilation
[Ref.: #66611]	maltose ChEBI	+/-	growth
[Ref.: #66611]	melibiose ChEBI	+/-	growth
[Ref.: #66611]	myo-inositol ChEBI	+	carbon source
[Ref.: #66611]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #66611]	nitrate ChEBI	+	reduction
[Ref.: #33961]	nitrate ChEBI	+	builds gas from
[Ref.: #33961]	nitrate ChEBI	+	reduction
[Ref.: #33961]	nitrite ChEBI	+	builds gas from
[Ref.: #33961]	nitrite ChEBI	-	reduction
[Ref.: #66611]	propionate ChEBI	+	carbon source
[Ref.: #66611]	putrescine ChEBI	+	carbon source
[Ref.: #66611]	salicin ChEBI	-	growth
[Ref.: #66611]	sarcosine ChEBI	+	carbon source
[Ref.: #66611]	sodium acetate ChEBI	+	carbon source
[Ref.: #66611]	sodium citrate ChEBI	+	carbon source
[Ref.: #66611]	sodium lactate ChEBI	+	carbon source
[Ref.: #66611]	sodium pyruvate ChEBI	+	carbon source
[Ref.: #66611]	sodium succinate ChEBI	+	carbon source
[Ref.: #66611]	starch ChEBI	+	hydrolysis
[Ref.: #66611]	sucrose ChEBI	+	carbon source
[Ref.: #66611]	trans-aconitate ChEBI	+	carbon source
[Ref.: #66611]	trehalose ChEBI	-	growth
[Ref.: #66611]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66611]		indole ChEBI	no
[Ref.: #33961]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #33961]		acetoin ChEBI	-
[Ref.: #33961]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #66611]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #33961]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #66611]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #33961]	amylase	-
[Ref.: #66611]	arginine dihydrolase	-	3.5.3.6
[Ref.: #33961]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #33961]	caseinase	-	3.4.21.50
[Ref.: #66611]	catalase	+	1.11.1.6
[Ref.: #33961]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #33961]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #33961]	gelatinase	+/-
[Ref.: #33961]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #33961]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #33961]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #33961]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #33961]	oxidase	+
[Ref.: #33961]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #33961]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #33961]	tryptophan deaminase	-
[Ref.: #33961]	tween esterase	-
[Ref.: #66611]	urease	-	3.5.1.5
[Ref.: #33961]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #33961]	11154	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	-	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	100	12 of 12
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	allantoin degradation	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	tryptophan metabolism	86.84	33 of 38
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tyrosine metabolism	85.71	12 of 14
[Ref.: #66794]	purine metabolism	85.11	80 of 94
[Ref.: #66794]	phenol degradation	85	17 of 20
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lysine metabolism	76.19	32 of 42
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	carnitine metabolism	75	6 of 8
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
		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.: #66611]	Sample type/isolated from	oysters on the coast of Vinaroz
[Ref.: #66611]	Sampling date	May, 1990
[Ref.: #66611]	Geographic location (country and/or sea, region)	Western Mediterranean coast
[Ref.: #66611]	Country	Spain
[Ref.: #66611]	Country ISO 3 Code	ESP
[Ref.: #66611]	Continent	Europe
[Ref.: #66611]	Geographic location	40.4566°/0.5266°
[Ref.: #66611]	Enrichment culture composition	The strain was isolated from homogenized, seawater-diluted oyster meat, inoculated on the surface of a marine agar (MA, Difco) plate.
[Ref.: #66611]	Enrichment culture duration	10 days
[Ref.: #66611]	Enrichment culture temperature	28 ̊C

[Ref.: #33961]	Sample type/isolated from	Animal, Oyster meat
[Ref.: #33961]	Geographic location (country and/or sea, region)	Valencia
[Ref.: #33961]	Country	Spain
[Ref.: #33961]	Country ISO 3 Code	ESP
[Ref.: #33961]	Continent	Europe
[Ref.: #33961]	Isolation date	1990

[Ref.: #33961]	Geographic location (country and/or sea, region)	Valencia
[Ref.: #33961]	Country	Spain
[Ref.: #33961]	Country ISO 3 Code	ESP
[Ref.: #33961]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Coast
#Host	#Invertebrates (Other)	#Mollusca

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence MH023307 (>99% sequence identity) for Ruegeria from Microbeatlas

Aquatic Samples	4771
Soil Samples	60
Animal Samples	398
Plant Samples	22
Total Samples	5251

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

[Ref.: #33961]

Biosafety level

Risk group (French classification)

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.: #66611]	Ruegeria sp. CECT 5091 16S ribosomal RNA gene, partial sequence	MH023307	1419	ENA	1715692 tax ID
[Ref.: #66611]	Ruegeria denitrificans strain CECT 5091, whole genome shotgun sequencing project	CYUD00000000	42	ENA	1715692 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ruegeria denitrificans CECT 5091	GCA_001458295	contig	GenBank	1715692 tax ID	*
[Ref.: #66792]	Ruegeria sp. CECT 5091	1715692.3	wgs	PATRIC	1715692 tax ID	*
[Ref.: #66792]	Ruegeria denitrificans CECT 5091	2713896969	draft	JGI IMG/M	1715692 tax ID	*

[Ref.: #66611]

GC-content

56.70 mol%

sequence analysis

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: Ruegeria sp. CECT 5091 PATRIC: 1715692.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ruegeria sp. CECT 5091 PATRIC: 1715692.3
[Ref.: #69480]	motile	no	62.101	yes
[Ref.: #69480]	gram-positive	no	98.182	no
[Ref.: #69480]	anaerobic	no	98.538	yes
[Ref.: #69480]	aerobic	yes	91.09	yes
[Ref.: #69480]	halophile	yes	79.922	no
[Ref.: #69480]	spore-forming	no	95.767	no
[Ref.: #69480]	glucose-util	yes	69.929	yes
[Ref.: #69480]	flagellated	no	81.679	no
[Ref.: #69480]	thermophile	no	96.146	yes
[Ref.: #69480]	glucose-ferment	no	91.827	no

Availability in culture collections External links

[Ref.: #33961]

Culture collection no.

CIP 108403, CECT 5091, LMG 29896

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis.	Arahal DR, Lucena T, Rodrigo-Torres L, Pujalte MJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002867	2018	*

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 )

#33961 Collection of Institut Pasteur ; Curators of the CIP; CIP 108403

#66611

David R. Arahal, Teresa Lucena, Lidia Rodrigo-Torres, Maria J. Pujalte: Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis. IJSEM 68: 2515 - 2522 2018 ( DOI 10.1099/ijsem.0.002867 , PubMed 29944092 )

#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 .

#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 )

* These data were automatically processed and therefore are not curated

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Search for species Ruegeria denitrificans in external resources:
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Ruegeria sp. CECT 5091

Ruegeria sp. CECT 5091

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