Variovorax paradoxus (DSM 30034, ATCC 17713, DSM 66)

Name: Variovorax paradoxus (DSM 30034, ATCC 17713, DSM 66)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3008

Type strain

Strain Designation 351, B13-0-1 D, B13-0-1D

Culture col. no. DSM 30034 ATCC 17713 DSM 66 IFO 15149 NBRC 15149 14 more

NCBI tax ID(s) 1321610 34073

Special Collections DSMZ CCUG JCM CIP JMRC

History DSMZ <- ATCC <- R.Y. Stanier, 351 <- D.H. Davis, B13-0-1 D JCM <-- IAM 12373 <-- ATCC 17713 <-- R. Y. Stanier 351 <-- D. Davis 13-0-1D. CIP <- 1991, CCUG <- ATCC <- R.Y. Stanier, Inst. Pasteur, Paris, France: strain 351, Alcaligenes paradoxus biotype I <- D.H. Davis: strain B13-0-1D

Links

Variovorax paradoxus 351 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 5036

LMG 1797,ATCC 17713,CCUG 1777,DSM 30034,DSM 66,IAM 12373,IAM 13535,CIP 103459,NCIB 11964,IFO 15149,NCIMB 11964,CCM 4467,VKM B-1329,KCTC 1007,NBRC 15149,BCRC 17070,CCRC 17070,KCTC 12459,KACC 10222,JCM 20526,JCM 20895

@ref 20215

Last LPSN update 2026-05-29 08:25:36

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Variovorax

Species Variovorax paradoxus

Full scientific name Variovorax paradoxus (Davis 1969) Willems et al. 1991

Synonyms (1)

Alcaligenes paradoxus

BacDive ID	Other strains from **Variovorax paradoxus** (21)	Type strain
3000	V. paradoxus 12-6-2, 350, DSM 645, ATCC 17712, CCUG 15916, ...
3001	V. paradoxus 14-O-1, 353, CCUG 15917, DSM 646, ATCC 17715, ...
3002	V. paradoxus 3-20-2, 360, DSM 647, ATCC 17722, JCM 20897, ...
3003	V. paradoxus 444, DSM 1070, ICPB 2921-444, CCUG 15918, ...
3004	V. paradoxus DSM 1071, ICPB 2922-447, JCM 20899, IAM 13539
3005	V. paradoxus DSM 1072, ICPB 2923-449
3006	V. paradoxus JMP116, pJP1, DSM 4065
3007	V. paradoxus R1L1, DSM 16541
3009	V. paradoxus 180, P2-106-S (3), CCUG 1778, LMG 1796, DSM ...
3010	V. paradoxus B4, DSM 21786
22977	V. paradoxus BF3, DSM 9258
100654	V. paradoxus SF004496,
144086	V. paradoxus CCUG 22893, ATCC 17719, LMG 3577, JCM 20912, ...
154267	V. paradoxus CCUG 52932
156597	V. paradoxus CCUG 63252
156689	V. paradoxus CCUG 64149
156834	V. paradoxus CCUG 65978
156843	V. paradoxus CCUG 66021
163007	V. paradoxus JCM 20910, ATCC 17716, IAM 13550, LMG 3574
163008	V. paradoxus JCM 20911, ATCC 17718, IAM 13551, LMG 3576
169152	V. paradoxus IDSBO-4, DSM 113672

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121552	negative	rod-shaped
125439	negative		94.886
125438	negative		97.3

Colony morphology

121552

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
36606	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
9096	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)	Medium recipe at MediaDive	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
9096	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
121552	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
9096	positive	growth	30
36606	positive	growth	25
44417	positive	growth	30
67770	positive	growth	25
121552	positive	growth	15-37
121552	negative	growth	5
121552	negative	growth	41
121552	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44417	aerobe
121552	obligate aerobe
125439	obligate aerobe	99.881

Spore formation

@ref	Spore formation	Confidence
125439		98.914

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121552	NaCl	positive	growth	0-2 %
121552	NaCl		growth	4 %
121552	NaCl		growth	6 %
121552	NaCl		growth	8 %
121552	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68374	29016 ChEBI	arginine	-	hydrolysis	from API ID32E
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68374	17057 ChEBI	cellobiose	-	builds acid from	from API ID32E
121552	16947 ChEBI	citrate	-	carbon source
68374	18333 ChEBI	D-arabitol	-	builds acid from	from API ID32E
68374	18024 ChEBI	D-galacturonic acid	-	builds acid from	from API ID32E
68374	17634 ChEBI	D-glucose	-	builds acid from	from API ID32E
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68374	16899 ChEBI	D-mannitol	-	builds acid from	from API ID32E
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
121552	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
121552	606565 ChEBI	hippurate	-	hydrolysis
68374	30849 ChEBI	L-arabinose	-	builds acid from	from API ID32E
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68374	18403 ChEBI	L-arabitol	-	builds acid from	from API ID32E
68374	62345 ChEBI	L-rhamnose	-	builds acid from	from API ID32E
68374	25094 ChEBI	lysine	-	degradation	from API ID32E
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68374	15792 ChEBI	malonate	-	assimilation	from API ID32E
121552	15792 ChEBI	malonate	+	assimilation
68374	17306 ChEBI	maltose	-	builds acid from	from API ID32E
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68374	17268 ChEBI	myo-inositol	-	builds acid from	from API ID32E
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
121552	17632 ChEBI	nitrate	-	builds gas from
121552	17632 ChEBI	nitrate	+	reduction
121552	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121552	16301 ChEBI	nitrite	-	builds gas from
121552	16301 ChEBI	nitrite	-	reduction
68374	18257 ChEBI	ornithine	-	degradation	from API ID32E
68374	18394 ChEBI	palatinose	-	builds acid from	from API ID32E
68374	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API ID32E
68374	15963 ChEBI	ribitol	-	builds acid from	from API ID32E
68374	30911 ChEBI	sorbitol	-	builds acid from	from API ID32E
68374	17992 ChEBI	sucrose	-	builds acid from	from API ID32E
68374	27082 ChEBI	trehalose	-	builds acid from	from API ID32E
68374	27897 ChEBI	tryptophan	-	energy source	from API ID32E
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68374	16199 ChEBI	urea	-	hydrolysis	from API ID32E
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121552	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite
68369	35581 ChEBI	indole	from API 20NE
68374	35581 ChEBI	indole	from API ID32E
121552	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
121552	15688 ChEBI	acetoin		-
121552	17234 ChEBI	glucose			-
68374	35581 ChEBI	indole	-			from API ID32E
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
121552	alcohol dehydrogenase	-	1.1.1.1
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
68374	alpha-galactosidase	-	3.2.1.22	from API ID32E
68374	alpha-glucosidase	+	3.2.1.20	from API ID32E
68374	alpha-maltosidase	-		from API ID32E
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121552	amylase	-
68374	arginine dihydrolase	-	3.5.3.6	from API ID32E
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
121552	beta-galactosidase	-	3.2.1.23
68374	beta-galactosidase	-	3.2.1.23	from API ID32E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68374	beta-glucosidase	-	3.2.1.21	from API ID32E
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68374	beta-glucuronidase	-	3.2.1.31	from API ID32E
121552	caseinase	-	3.4.21.50
121552	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
121552	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121552	gamma-glutamyltransferase	+	2.3.2.2
121552	gelatinase	-
68369	gelatinase	-		from API 20NE
68374	L-aspartate arylamidase	+	3.4.11.21	from API ID32E
121552	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121552	lipase	-
68374	lipase	-		from API ID32E
68382	lipase (C 14)	-		from API zym
121552	lysine decarboxylase	-	4.1.1.18
68374	lysine decarboxylase	-	4.1.1.18	from API ID32E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68374	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API ID32E
121552	ornithine decarboxylase	-	4.1.1.17
68374	ornithine decarboxylase	-	4.1.1.17	from API ID32E
121552	oxidase	+
121552	phenylalanine ammonia-lyase	-	4.3.1.24
121552	protease	-
68382	trypsin	-	3.4.21.4	from API zym
121552	tryptophan deaminase	-
121552	tween esterase	-
121552	urease	+	3.5.1.5
68374	urease	-	3.5.1.5	from API ID32E
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	4-hydroxymandelate degradation	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	methanofuran biosynthesis	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	palmitate biosynthesis	100	22 of 22
66794	gallate degradation	100	5 of 5
66794	photosynthesis	100	14 of 14
66794	ketogluconate metabolism	100	8 of 8
66794	valine metabolism	100	9 of 9
66794	resorcinol degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	IAA biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	ceramide biosynthesis	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cyanate degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	taurine degradation	100	1 of 1
66794	NAD metabolism	94.44	17 of 18
66794	citric acid cycle	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
66794	phenol degradation	90	18 of 20
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	3-phenylpropionate degradation	86.67	13 of 15
66794	purine metabolism	86.17	81 of 94
66794	propanol degradation	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	methionine metabolism	84.62	22 of 26
66794	tryptophan metabolism	84.21	32 of 38
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	alanine metabolism	82.76	24 of 29
66794	glycolysis	82.35	14 of 17
66794	proline metabolism	81.82	9 of 11
66794	lysine metabolism	80.95	34 of 42
66794	vitamin K metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	degradation of sugar acids	80	20 of 25
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	lipid A biosynthesis	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	oxidative phosphorylation	73.63	67 of 91
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	tyrosine metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	arginine metabolism	70.83	17 of 24
66794	vitamin B1 metabolism	69.23	9 of 13
66794	sulfate reduction	69.23	9 of 13
66794	degradation of pentoses	67.86	19 of 28
66794	acetoin degradation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	allantoin degradation	66.67	6 of 9
66794	cysteine metabolism	66.67	12 of 18
66794	sulfoquinovose degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	histidine metabolism	65.52	19 of 29
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	degradation of sugar alcohols	62.5	10 of 16
66794	hydrogen production	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	glycine betaine biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	carnitine metabolism	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	cholesterol biosynthesis	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	carotenoid biosynthesis	45.45	10 of 22
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	methanogenesis from CO2	41.67	5 of 12
66794	vitamin B12 metabolism	41.18	14 of 34
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

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
44417	-	+	+	+	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-
121552	-	+	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
44417	+	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	+	+	-	-	+

API ID32E

@ref	ODC	ADH (Arg)	LDC (Lys)	URE	LARL	GAT	5KG	LipaseLIP	Phenol red (Acidification)RP	beta GLU	MAN	MAL	ADO	PLE	beta GUR	MNT	IND	N-Acetyl-beta-Glucosaminidasebeta NAG	beta GAL	GLU	SAC	LARA	DARL	alpha GLU	alpha GAL	TRE	RHA	INO	CEL	SOR	alpha-MaltosidasealphaMAL	L-aspartic acid arylamidaseAspA
44417	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121552	not determinedn.d.	+	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	+	-	+	+	-	-	-	+	-	+	-	-	+	+	-	-	-	-	-	-	-	-	+	-	+	+	-	-	-	-	+	-	+	+	+	-	+	-	+	+	+	+	+	-	-	+	-	-	-	+	-	+	+	-	+	+	+	+	+	-	-	-	-	+	+	+	+	+	-	+	+	+	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
9096	soil
44417	Soil in mineral medium with an atmosphere of H2...	USA	USA	North America
67770	Soil
121552	Environment, Soil enriched with pantothenate

Taxonmaps

69479

Global distribution of 16S sequence D88006 (>99% sequence identity) for Variovorax from Microbeatlas

Aquatic Samples	2157
Soil Samples	3106
Animal Samples	2122
Plant Samples	2332
Total Samples	9717

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9096	1	Risk group (German classification) According to TRBA 466
121552	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
124043	ASM4830512v1 assembly for Variovorax paradoxus NBRC 15149	complete	GCA_048305125			1321610	98.49
67770	ASM159136v1 assembly for Variovorax paradoxus NBRC 15149	contig	GCA_001591365	1321610.3	2731957648	1321610	76.36

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Variovorax paradoxus gene for 16S rRNA, partial sequence, strain: DSM 30034	AB622219	1483	34073
20218	Variovorax paradoxus DNA, 16S-23S rRNA gene internal transcribed spacer, strain: DSM 30034	AB622229	634	34073
20218	Variovorax paradoxus 16S rRNA gene, strain DSM 66	AJ420329	1483	34073
20218	Variovorax paradoxus gene for 16S ribosomal RNA	D30793	1457	34073
20218	Variovorax paradoxus DNA for 16S ribosomal RNA	D88006	1467	34073
20218	Variovorax paradoxus gene for 16S rRNA, partial sequence, strain: NBRC 15149	AB680784	1460	1321610

GC content

@ref	GC-content (mol%)	Method
9096	67.0	thermal denaturation, midpoint method (Tm)
9096	68.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4830512v1 assembly for Variovorax paradoxus NBRC 15149
NCBI: GCA_048305125

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.88	no
125439	gram_stain	BacteriaNetⓘ	negative	94.89	no
125439	motility	BacteriaNetⓘ	yes	76.56	no
125439	spore_formation	BacteriaNetⓘ	no	98.91	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Variovorax paradoxus NBRC 15149
PATRIC: 1321610.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.30	no
125438	anaerobic	anaerobicⓘ	no	96.53	yes
125438	spore-forming	spore-formingⓘ	no	87.30	no
125438	aerobic	aerobicⓘ	yes	88.70	yes
125438	thermophilic	thermophileⓘ	no	99.99	yes
125438	flagellated	motile2+ⓘ	yes	81.01	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Substrate binding and catalytic mechanism of the Se-glycosyltransferase SenB in the biosynthesis of selenoneine.	Huang W, Song J, Sun T, He Y, Li X, Deng Z, Long F.	Nat Commun	10.1038/s41467-024-46065-6	2024
	Semirational Design of SenC to Enhance Organic Selenium Biosynthesis.	Shao K, Yu X, Zhao Y, Zhang Y, Liu X.	Microb Biotechnol	10.1111/1751-7915.70130	2025
Metabolism	Morphological and Metabolite Responses of Potatoes under Various Phosphorus Levels and Their Amelioration by Plant Growth-Promoting Rhizobacteria.	Chea L, Pfeiffer B, Schneider D, Daniel R, Pawelzik E, Naumann M.	Int J Mol Sci	10.3390/ijms22105162	2021
	Sequence-Based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families.	Maimanakos J, Chow J, Gassmeyer SK, Gullert S, Busch F, Kourist R, Streit WR.	Front Microbiol	10.3389/fmicb.2016.01332	2016
Metabolism	OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes.	Saraiva JP, Bartholomaus A, Kallies R, Gomes M, Bicalho M, Coelho Kasmanas J, Vogt C, Chatzinotas A, Stadler P, Dias O, Nunes da Rocha U.	Life Sci Alliance	10.26508/lsa.202101167	2021
Metabolism	Ambient nitrogen reduction cycle using a hybrid inorganic-biological system.	Liu C, Sakimoto KK, Colon BC, Silver PA, Nocera DG.	Proc Natl Acad Sci U S A	10.1073/pnas.1706371114	2017
Metabolism	Metabolism of acyl-homoserine lactone quorum-sensing signals by Variovorax paradoxus.	Leadbetter JR, Greenberg EP.	J Bacteriol	10.1128/jb.182.24.6921-6926.2000	2000
	The extent of functional redundancy changes as species' roles shift in different environments.	Fetzer I, Johst K, Schawe R, Banitz T, Harms H, Chatzinotas A.	Proc Natl Acad Sci U S A	10.1073/pnas.1505587112	2015
Metabolism	Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography.	Ginige MP, Keller J, Blackall LL.	Appl Environ Microbiol	10.1128/aem.71.12.8683-8691.2005	2005
Metabolism	Aerobic degradation of mercaptosuccinate by the gram-negative bacterium Variovorax paradoxus strain B4.	Carbajal-Rodriguez I, Stoveken N, Satola B, Wubbeler JH, Steinbuchel A.	J Bacteriol	10.1128/jb.00793-10	2011
	Differential Impacts of Willow and Mineral Fertilizer on Bacterial Communities and Biodegradation in Diesel Fuel Oil-Contaminated Soil.	Leewis MC, Uhlik O, Fraraccio S, McFarlin K, Kottara A, Glover C, Macek T, Leigh MB.	Front Microbiol	10.3389/fmicb.2016.00837	2016
	Whole-genome sequences of 38 siderophore-producing isolates from root systems of two pea and one wheat varieties.	Zhu L, Lopez-Roques C, Sallaberry M, Jason K, Ouerdane L, Mazurier S, Lemanceau P, Pivato B.	Microbiol Resour Announc	10.1128/mra.00570-25	2025
Genetics	Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660.	Ghimire N, Kim B, Lee CM, Oh TJ.	BMC Genomics	10.1186/s12864-022-08589-3	2022
	Potential of Variovorax paradoxus isolate BFB1_13 for bioremediation of BTEX contaminated sites.	Benedek T, Szentgyorgyi F, Gergocs V, Menashe O, Gonzalez PAF, Probst AJ, Kriszt B, Tancsics A.	AMB Express	10.1186/s13568-021-01289-3	2021
	Complete Genome Sequences of Pseudomonas alkylphenolica Neo and Variovorax sp. Strain CSUSB, Obtained in Undergraduate Microbiology Courses Using a Hybrid Assembly Approach.	Ne Ville C, Enright D, Hernandez I, Dodsworth J, Orwin P.	Microbiol Resour Announc	10.1128/mra.01520-19	2020
	Enrichment and Analysis of Stable 1,4-dioxane-Degrading Microbial Consortia Consisting of Novel Dioxane-Degraders.	Tusher TR, Shimizu T, Inoue C, Chien MF.	Microorganisms	10.3390/microorganisms8010050	2019
Genetics	Selective enrichment, identification, and isolation of diclofenac, ibuprofen, and carbamazepine degrading bacteria from a groundwater biofilm.	Papai M, Benedek T, Tancsics A, Bornemann TLV, Plewka J, Probst AJ, Hussein D, Maroti G, Menashe O, Kriszt B.	Environ Sci Pollut Res Int	10.1007/s11356-022-24975-6	2023
Metabolism	Production of ethanol from mannitol by the yeast strain Saccharomyces paradoxus NBRC 0259.	Ota A, Kawai S, Oda H, Iohara K, Murata K.	J Biosci Bioeng	10.1016/j.jbiosc.2013.03.018	2013
	Prevalence and Correlates of Phenazine Resistance in Culturable Bacteria from a Dryland Wheat Field.	Perry EK, Newman DK.	Appl Environ Microbiol	10.1128/aem.02320-21	2022
	Screening of Endophytic Bacteria of Leucojum aestivum 'Gravety Giant' as a Potential Source of Alkaloids and as Antagonist to Some Plant Fungal Pathogens.	Munakata Y, Spina R, Slezack-Deschaumes S, Genestier J, Hehn A, Laurain-Mattar D.	Microorganisms	10.3390/microorganisms10102089	2022
	A Salt-Tolerant Streptomyces paradoxus D2-8 from Rhizosphere Soil of Phragmites communis Augments Soybean Tolerance to Soda Saline-Alkali Stress.	Gao Y, Han Y, Li X, Li M, Wang C, Li Z, Wang Y, Wang W.	Pol J Microbiol	10.33073/pjm-2022-006	2022
	Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the candidate division FBP.	Kobayashi K, Aoyagi H.	PeerJ	10.7717/peerj.7876	2019
Metabolism	Regulation of pH attenuates toxicity of a byproduct produced by an ethanologenic strain of Sphingomonas sp. A1 during ethanol fermentation from alginate.	Fujii M, Yoshida S, Murata K, Kawai S.	Bioengineered	10.4161/bioe.27397	2014
Metabolism	Biofuel Production Based on Carbohydrates from Both Brown and Red Macroalgae: Recent Developments in Key Biotechnologies.	Kawai S, Murata K.	Int J Mol Sci	10.3390/ijms17020145	2016
	Novel Conopeptides of Largely Unexplored Indo Pacific Conus sp.	Lebbe EK, Ghequire MG, Peigneur S, Mille BG, Devi P, Ravichandran S, Waelkens E, D'Souza L, De Mot R, Tytgat J.	Mar Drugs	10.3390/md14110199	2016
Metabolism	The antimicrobial compound xantholysin defines a new group of Pseudomonas cyclic lipopeptides.	Li W, Rokni-Zadeh H, De Vleeschouwer M, Ghequire MG, Sinnaeve D, Xie GL, Rozenski J, Madder A, Martins JC, De Mot R.	PLoS One	10.1371/journal.pone.0062946	2013
Phylogeny	Seasonal change in bacterial flora and biomass in mountain snow from the Tateyama Mountains, Japan, analyzed by 16S rRNA gene sequencing and real-time PCR.	Segawa T, Miyamoto K, Ushida K, Agata K, Okada N, Kohshima S.	Appl Environ Microbiol	10.1128/aem.71.1.123-130.2005	2005
Enzymology	Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences.	Hiorns WD, Methe BA, Nierzwicki-Bauer SA, Zehr JP.	Appl Environ Microbiol	10.1128/aem.63.7.2957-2960.1997	1997
Phylogeny	Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core.	Sheridan PP, Miteva VI, Brenchley JE.	Appl Environ Microbiol	10.1128/aem.69.4.2153-2160.2003	2003
Enzymology	Gene cloning of alpha-methylserine aldolase from Variovorax paradoxus and purification and characterization of the recombinant enzyme.	Nozaki H, Kuroda S, Watanabe K, Yokozeki K	Biosci Biotechnol Biochem	10.1271/bbb.80274	2008
	Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov.	Jin CZ, Zhuo Y, Wu X, Ko SR, Li T, Jin FJ, Ahn CY, Oh HM, Lee HG, Jin L.	Microorganisms	10.3390/microorganisms8020262	2020
Phylogeny	Variovorax gossypii sp. nov., isolated from Gossypium hirsutum.	Kampfer P, Busse HJ, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijsem.0.000581	2015
Phylogeny	Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere.	Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JG	Antonie Van Leeuwenhoek	10.1007/s10482-014-0304-3	2014
Phylogeny	Variovorax defluvii sp. nov., isolated from sewage.	Jin L, Kim KK, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijs.0.035295-0	2011
Phylogeny	Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.	Miwa H, Ahmed I, Yoon J, Yokota A, Fujiwara T	Int J Syst Evol Microbiol	10.1099/ijs.0.65315-0	2008
Phylogeny	Variovorax soli sp. nov., isolated from greenhouse soil.	Kim BY, Weon HY, Yoo SH, Lee SY, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64390-0	2006
Phylogeny	Variovorax dokdonensis sp. nov., isolated from soil.	Yoon JH, Kang SJ, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64070-0	2006
Phylogeny	Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity.	Woo CY, Kim J	J Microbiol Biotechnol	10.4014/jmb.2205.05018	2022

References

#9096	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30034
#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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#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 )
#36606	; Curators of the CIP;
#44417	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 1777
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68374	Automatically annotated from API ID32E .
#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 .
#121552	Collection of Institut Pasteur ; Curators of the CIP; CIP 103459
#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 )

Content

About us

Variovorax paradoxus (DSM 30034, ATCC 17713, DSM 66)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20NE

API ID32E

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_048305125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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