Ruegeria denitrificans (CIP 108403, CECT 5091, 5OM10)

Name: Ruegeria denitrificans (CIP 108403, CECT 5091, 5OM10)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 135100

Type strain

Strain Designation 5OM10

Culture col. no. CIP 108403 CECT 5091 5OM10 LMG 29896

NCBI tax ID(s) 1715692

Special Collections CIP Literature strains

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

Links

Ruegeria denitrificans 5OM10 is an aerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies.

Gram-negative coccus-shaped colony-forming aerobe chemoorganotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 301629

LMG 29896,CECT 5091,CIP 108403

@ref 20215

Last LPSN update 2026-02-09 11:32:21

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Ruegeria

Species Ruegeria denitrificans

Full scientific name Ruegeria denitrificans Arahal et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
66611	negative	coccus-shaped
125438	negative		98.833
125439	negative		95.3
33961	negative	rod-shaped

Colony morphology

@ref	Colony shape	Medium used
66611	circular	Marine agar (MA)
33961

Pigmentation

66611

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Composition	Medium link
33961	Marine agar (MA)	Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
66611	Marine agar (MA)
33961	CIP Medium 13		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
33961	positive	growth	25
33961	negative	growth	41
33961	negative	growth	37
33961	negative	growth	5
33961	positive	growth	15-30
33961	negative	growth	45
66611	negative	growth	37
66611	positive	optimum	26
66611	positive	optimum	15
66611	negative	growth	4

Culture pH

@ref	Ability	Type	PH	PH range
66611	positive	optimum	7
66611	positive	growth	6-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
66611	aerobe
125439	aerobe	94.7

Nutrition type

66611

Typechemoorganotroph

Spore formation

@ref	Spore formation	Confidence
125438		92.867
125439		95.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66611	Marine salts	positive	growth	1.5-6 %
66611	Marine salts	positive	optimum	3 %
66611	Marine salts		growth	1 %
66611	NaCl		growth	7 %
33961	NaCl		growth	0 %
33961	NaCl		growth	2 %
33961	NaCl		growth	4 %
33961	NaCl		growth	6 %
33961	NaCl		growth	8 %
33961	NaCl		growth	10 %

Observation

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66611	16810 ChEBI	2-oxoglutarate	+	carbon source
66611	37054 ChEBI	3-hydroxybutyrate	+	carbon source
66611	30566 ChEBI	4-aminobutyrate	+	carbon source
66611	90259 ChEBI	4-nitrophenyl beta-D-glucopyranoside	+	hydrolysis
66611	27613 ChEBI	amygdalin	-	growth
66611	17968 ChEBI	butyrate	+	carbon source
66611		casein	+	hydrolysis
66611	17057 ChEBI	cellobiose	-	growth
33961	16947 ChEBI	citrate	-	carbon source
66611	15824 ChEBI	D-fructose	+/-	growth
66611	12936 ChEBI	D-galactose	+	carbon source
66611	18024 ChEBI	D-galacturonic acid	-	growth
66611	30612 ChEBI	D-glucarate	-	growth
66611	8391 ChEBI	D-gluconate	-	growth
66611	17634 ChEBI	D-glucose	+	carbon source
66611	15748 ChEBI	D-glucuronate	-	growth
66611	16659 ChEBI	D-glycerate	+	carbon source
66611	16899 ChEBI	D-mannitol	+	carbon source
66611	16024 ChEBI	D-mannose	+	carbon source
66611	16988 ChEBI	D-ribose	+	carbon source
66611	17924 ChEBI	D-sorbitol	+	carbon source
66611	65327 ChEBI	D-xylose	-	growth
66611	16991 ChEBI	dna	+	hydrolysis
66611	4853 ChEBI	esculin	+	hydrolysis
33961	4853 ChEBI	esculin	-	hydrolysis
66611	5291 ChEBI	gelatin	+	hydrolysis
33961	17234 ChEBI	glucose	+/-	degradation
66611	17754 ChEBI	glycerol	+	carbon source
66611	15428 ChEBI	glycine	+/-	growth
33961	606565 ChEBI	hippurate	-	hydrolysis
66611	16977 ChEBI	L-alanine	+	carbon source
66611	30849 ChEBI	L-arabinose	-	growth
66611	16467 ChEBI	L-arginine	+	carbon source
66611	29991 ChEBI	L-aspartate	+	carbon source
66611	16349 ChEBI	L-citrulline	+	carbon source
66611	29985 ChEBI	L-glutamate	+	carbon source
66611	15971 ChEBI	L-histidine	-	growth
66611	15603 ChEBI	L-leucine	+	carbon source
66611	18019 ChEBI	L-lysine	+	carbon source
66611	15729 ChEBI	L-ornithine	+	carbon source
66611	62345 ChEBI	L-rhamnose	+	carbon source
66611	17115 ChEBI	L-serine	+	carbon source
66611	16857 ChEBI	L-threonine	+	carbon source
66611	17895 ChEBI	L-tyrosine	+	carbon source
66611	17716 ChEBI	lactose	-	growth
66611	25115 ChEBI	malate	+	carbon source
33961	15792 ChEBI	malonate	-	assimilation
66611	17306 ChEBI	maltose	+/-	growth
66611	28053 ChEBI	melibiose	+/-	growth
66611	17268 ChEBI	myo-inositol	+	carbon source
66611	59640 ChEBI	N-acetylglucosamine	+	carbon source
66611	17632 ChEBI	nitrate	+	reduction
33961	17632 ChEBI	nitrate	+	builds gas from
33961	17632 ChEBI	nitrate	+	reduction
33961	16301 ChEBI	nitrite	+	builds gas from
33961	16301 ChEBI	nitrite	-	reduction
66611	17272 ChEBI	propionate	+	carbon source
66611	17148 ChEBI	putrescine	+	carbon source
66611	17814 ChEBI	salicin	-	growth
66611	15611 ChEBI	sarcosine	+	carbon source
66611	32954 ChEBI	sodium acetate	+	carbon source
66611	53258 ChEBI	sodium citrate	+	carbon source
66611	75228 ChEBI	sodium lactate	+	carbon source
66611	50144 ChEBI	sodium pyruvate	+	carbon source
66611	63675 ChEBI	sodium succinate	+	carbon source
66611	28017 ChEBI	starch	+	hydrolysis
66611	17992 ChEBI	sucrose	+	carbon source
66611	15708 ChEBI	trans-aconitate	+	carbon source
66611	27082 ChEBI	trehalose	-	growth
66611	53426 ChEBI	tween 80	+	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66611	35581 ChEBI	indole
33961	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
33961	15688 ChEBI	acetoin	-
33961	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
66611	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
33961	alcohol dehydrogenase	-	1.1.1.1
66611	alkaline phosphatase	+	3.1.3.1
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
33961	amylase	-
66611	arginine dihydrolase	-	3.5.3.6
68382	beta-galactosidase	+	3.2.1.23	from API zym
33961	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
33961	caseinase	-	3.4.21.50
66611	catalase	+	1.11.1.6
33961	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
33961	gamma-glutamyltransferase	+	2.3.2.2
33961	gelatinase	+/-
33961	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
33961	lipase	-
68382	lipase (C 14)	-		from API zym
33961	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
33961	ornithine decarboxylase	-	4.1.1.17
33961	oxidase	+
33961	phenylalanine ammonia-lyase	-	4.3.1.24
33961	protease	-
68382	trypsin	-	3.4.21.4	from API zym
33961	tryptophan deaminase	-
33961	tween esterase	-
66611	urease	-	3.5.1.5
33961	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

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

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
33961	-	+	+	+	-	+	+	-	-	-	+	+	-	+	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Coast
#Host	#Invertebrates (Other)	#Mollusca

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation date
33961			Valencia	Spain	ESP	Europe
66611	oysters on the coast of Vinaroz	May, 1990	Western Mediterranean coast	Spain	ESP	Europe	40.4566	0.5266 40.4566/0.5266	The strain was isolated from homogenized, seawater-diluted oyster meat, inoculated on the surface of a marine agar (MA, Difco) plate.	10 days	28
33961	Animal, Oyster meat		Valencia	Spain	ESP	Europe						1990

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
33961	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Ruegeria_sp._CECT5091_Spades_Prokka assembly for Ruegeria denitrificans CECT 5091	contig	GCA_001458295	1715692.3	2713896969	1715692	69.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66611	Ruegeria denitrificans strain CECT 5091 16S ribosomal RNA gene, partial sequence	MH023307	1419		1715692

GC content

@ref	GC-content (mol%)	Method
66611	56.70	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ruegeria denitrificans CECT 5091
NCBI: GCA_001458295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	yes	63.30	no
125439	gram_stain	BacteriaNetⓘ	negative	95.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ruegeria sp. CECT 5091
PATRIC: 1715692.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	yes
125438	anaerobic	anaerobicⓘ	no	92.24	no
125438	spore-forming	spore-formingⓘ	no	92.87	no
125438	aerobic	aerobicⓘ	yes	85.66	yes
125438	thermophilic	thermophileⓘ	no	96.33	yes
125438	flagellated	motile2+ⓘ	no	52.51	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.	Isokpehi RD, Kim Y, Krejci SE, Trivedi VD.	Microorganisms	10.3390/microorganisms12040791	2024
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 .
#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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Ruegeria denitrificans (CIP 108403, CECT 5091, 5OM10)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001458295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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