Name: Sphingobium cloacae S-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14181

Type strain:

Species: Sphingobium cloacae

Strain Designation: S-3, S-3T

Culture col. no.: DSM 14926, CIP 107076, IAM 14885, JCM 10874, CCUG 54784, KCTC 12912

Strain history: CIP <- 2001, N. Urano, Tokyo Univ. Marine Science Technol., Tokyo, Japan: strain S-3T

NCBI tax ID(s): 120107 (species)

SI-ID 85290

LMG 21016, IAM 14885, JCM 10874, DSM 14926, CIP 107076, KCTC 12912, NBRC 102517, CIP 109372, CCUG 54784

Section

Sphingobium cloacae S-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from waste water of sewage plant.

Gram-negative
motile
rod-shaped
aerobe
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	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingobium*
	Species	**Sphingobium cloacae**
	Full Scientific Name (LPSN)	Sphingobium cloacae (Fujii et al. 2001) Prakash and Lal 2006

Synonym

Sphingomonas cloacae

Information on morphological and physiological properties Morphology

[Ref.: #118317]	Gram stain	negative

[Ref.: #118317]	Cell shape	rod-shaped

[Ref.: #118317]	Motility	yes

[Ref.: #60329]

Incubation period

3-4 days

[Ref.: #118317]	Pigment production	no
[Ref.: #118317]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5449]

Culture medium

MINERAL MEDIUM WITH VITAMINS (DSMZ Medium 462)

[Ref.: #5449]

Culture medium growth

[Ref.: #5449]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5449]

Culture medium composition

expand / minimize

[Ref.: #5449]

Culture medium

REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)

[Ref.: #5449]

Culture medium growth

[Ref.: #5449]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5449]

Culture medium composition

expand / minimize

[Ref.: #37530]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37530]

Culture medium growth

[Ref.: #37530]

Culture medium composition

expand / minimize

[Ref.: #39653]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #39653]

Culture medium growth

[Ref.: #39653]

Culture medium composition

expand / minimize

[Ref.: #118317]

Culture medium

CIP Medium 72

[Ref.: #118317]

Culture medium growth

[Ref.: #118317]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5449]		growth	28 °C
[Ref.: #37530]		growth	25 °C
[Ref.: #39653]		growth	25 °C
[Ref.: #60329]		growth	30 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #118317]		growth	25-37 °C
[Ref.: #118317]	no	growth	5 °C
[Ref.: #118317]	no	growth	10 °C
[Ref.: #118317]	no	growth	41 °C

[Ref.: #5449]	Temperature range	mesophilic
[Ref.: #37530]	Temperature range	mesophilic
[Ref.: #39653]	Temperature range	mesophilic
[Ref.: #60329]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #118317]	Temperature range	mesophilic
[Ref.: #118317]	Temperature range	psychrophilic
[Ref.: #118317]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #60329]	Oxygen tolerance	aerobe
[Ref.: #118317]	Oxygen tolerance	obligate aerobe

	Salt	Tested relation		Salt conc.
[Ref.: #118317]	NaCl		growth	0-4	%
[Ref.: #118317]	NaCl	no	growth	6	%
[Ref.: #118317]	NaCl	no	growth	8	%
[Ref.: #118317]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #118317]	citrate ChEBI	-	carbon source
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #118317]	esculin ChEBI	-	hydrolysis
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #118317]	nitrate ChEBI	-	reduction
[Ref.: #118317]	nitrate ChEBI	-	respiration
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #118317]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #118317]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #118317]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118317]	alcohol dehydrogenase	-	1.1.1.1
[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.: #118317]	amylase	-
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #118317]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE, API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118317]	caseinase	-	3.4.21.50
[Ref.: #118317]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #118317]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #118317]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #118317]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #118317]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #118317]	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.: #118317]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118317]	oxidase	+
[Ref.: #118317]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #118317]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118317]	tryptophan deaminase	-
[Ref.: #118317]	tween esterase	+
[Ref.: #118317]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #5449]	23211	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+
[Ref.: #5449]	23150	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+

API® Biotype100:

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

	API ID	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
[Ref.: #118317]	1988	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	+	-

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.: #118317]	10043	-	+	+	-	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	oxidative phosphorylation	46.15	42 of 91
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine 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.: #5449]	Sample type/isolated from	waste water of sewage plant
[Ref.: #5449]	Country	Japan
[Ref.: #5449]	Country ISO 3 Code	JPN
[Ref.: #5449]	Continent	Asia

[Ref.: #60329]	Sample type/isolated from	Sewage-treatment plant
[Ref.: #60329]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #60329]	Country	Japan
[Ref.: #60329]	Country ISO 3 Code	JPN
[Ref.: #60329]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sewage-treatment plant
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #118317]	Sample type/isolated from	Environment, Wastewater of a sewage treatment
[Ref.: #118317]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #118317]	Country	Japan
[Ref.: #118317]	Country ISO 3 Code	JPN
[Ref.: #118317]	Continent	Asia
[Ref.: #118317]	Isolation date	1999
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Plant (Factory)
#Engineered	#Waste	#Wastewater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB040739 (>99% sequence identity) for Sphingobium from Microbeatlas

Aquatic Samples	12
Soil Samples	5
Animal Samples	4
Plant Samples	6
Total Samples	27

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

[Ref.: #5449]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118317]	Biosafety level	1	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.: #5449]	Sphingobium cloacae gene for 16S ribosomal RNA, partial sequence	AB040739	1417	ENA	120107 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium cloacae JCM 10874	2802429338	complete	JGI IMG/M	120107 tax ID	*
[Ref.: #66792]	Sphingobium cloacae strain JCM 10874	120107.21	plasmid	PATRIC	120107 tax ID	*
[Ref.: #66792]	Sphingobium cloacae strain JCM 10874	120107.20	plasmid	PATRIC	120107 tax ID	*
[Ref.: #66792]	Sphingobium cloacae strain JCM 10874	120107.18	plasmid	PATRIC	120107 tax ID	*
[Ref.: #66792]	Sphingobium cloacae strain JCM 10874	120107.17	plasmid	PATRIC	120107 tax ID	*
[Ref.: #66792]	Sphingobium cloacae strain JCM 10874	120107.19	plasmid	PATRIC	120107 tax ID	*

[Ref.: #67770]

GC-content

63 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium cloacae JCM 10874 NCBI: GCA_002355855.1
[Ref.: #69480]	flagellated	no	88.496	no
[Ref.: #69480]	gram-positive	no	96.831	no
[Ref.: #69480]	anaerobic	no	98.956	yes
[Ref.: #69480]	aerobic	yes	93.474	yes
[Ref.: #69480]	halophile	no	95.266	no
[Ref.: #69480]	spore-forming	no	93.933	no
[Ref.: #69480]	glucose-util	yes	77.885	no
[Ref.: #69480]	thermophile	no	97.312	yes
[Ref.: #69480]	motile	yes	58.52	no
[Ref.: #69480]	glucose-ferment	no	94.043	yes

Availability in culture collections External links

[Ref.: #5449]

Culture collection no.

DSM 14926, CIP 107076, IAM 14885, JCM 10874, CCUG 54784, KCTC 12912

[Ref.: #83344]

SI-ID 85290

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Comparative Analysis of the Genetic Basis of Branched Nonylphenol Degradation by Sphingobium amiense DSM 16289(T) and Sphingobium cloacae JCM 10874(T).	Ootsuka M, Nishizawa T, Hasegawa M, Kurusu Y, Ohta H	Microbes Environ	10.1264/jsme2.ME18077	2018	*
Genetics	Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium cloacae JCM 10874T.	Ootsuka M, Nishizawa T, Ohta H	Genome Announc	10.1128/genomeA.01358-16	2016	*
Phylogeny	Sphingobium wenxiniae sp. nov., a synthetic pyrethroid (SP)-degrading bacterium isolated from activated sludge in an SP-manufacturing wastewater treatment facility.	Wang BZ, Guo P, Zheng JW, Hang BJ, Li L, He J, Li SP	Int J Syst Evol Microbiol	10.1099/ijs.0.023309-0	2010	*
Phylogeny	Sphingobium faniae sp. nov., a pyrethroid-degrading bacterium isolated from activated sludge treating wastewater from pyrethroid manufacture.	Guo P, Wang BZ, Hang BJ, Li L, Li SP, He J	Int J Syst Evol Microbiol	10.1099/ijs.0.009795-0	2009	*
Phylogeny	Sphingobium ummariense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium, isolated from HCH-contaminated soil.	Singh A, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.65712-0	2009	*
Phylogeny	Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov.	Prakash O, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.64080-0	2006	*
Phylogeny	Sphingomonas cloacae sp. nov., a nonylphenol-degrading bacterium isolated from wastewater of a sewage-treatment plant in Tokyo.	Fujii K, Urano N, Ushio H, Satomi M, Kimura S	Int J Syst Evol Microbiol	10.1099/00207713-51-2-603	2001	*

References

#5449

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14926

#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 )

#37530 ; Curators of the CIP;
#39653 ; Curators of the CIP;
#60329 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54784

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68369

Automatically annotated from API 20NE .

#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) .

#83344

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-ID85290.1 )

#118317 Collection of Institut Pasteur ; Curators of the CIP; CIP 107076
* These data were automatically processed and therefore are not curated

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