Sphingobium faniae (DSM 21829, CGMCC 1.7749, JZ-2)

Name: Sphingobium faniae (DSM 21829, CGMCC 1.7749, JZ-2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14196

Type strain

Strain Designation JZ-2

Culture col. no. DSM 21829 CGMCC 1.7749 JZ-2

NCBI tax ID(s) 570446

Special Collections DSMZ Literature strains

History <- P. Guo, Nanjing Agric. Univ., China; JZ-2

Links

Sphingobium faniae JZ-2 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from activated sludge of an aerobic, pyrethroid-contaminated wastewater.

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

Name and taxonomic classification

SI-ID 402233

DSM 21829

@ref 20215

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

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium faniae

Full scientific name Sphingobium faniae Guo et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29261	negative	1.15 µm	0.55 µm	rod-shaped
125438	negative				96.317
125439	negative				96.9

Pigmentation

29261

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15976	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15976	positive	growth	30
29261	positive	optimum	30

Culture pH

@ref	Ability	Type	PH
29261	positive	optimum	7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29261	aerobe
125439	aerobe	92.2

Spore formation

@ref	Spore formation	Confidence
29261
125439		96

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29261	NaCl	positive	growth	<1.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
29261	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
29261	27689 ChEBI	decanoate	+	carbon source
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
29261	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
29261	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
29261	29864 ChEBI	mannitol	+	carbon source
29261	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
29261	catalase	+	1.11.1.6
29261	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
29261	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	cyanate degradation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	butanoate fermentation	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	quinate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	95.45	21 of 22
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	propanol degradation	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	factor 420 biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	histidine metabolism	75.86	22 of 29
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	purine metabolism	73.4	69 of 94
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	phenol degradation	70	14 of 20
66794	Entner Doudoroff pathway	70	7 of 10
66794	pyrimidine metabolism	68.89	31 of 45
66794	methane metabolism	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	d-mannose degradation	66.67	6 of 9
66794	methionine metabolism	65.38	17 of 26
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	carnitine metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	cysteine metabolism	61.11	11 of 18
66794	polyamine pathway	60.87	14 of 23
66794	tryptophan metabolism	60.53	23 of 38
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	degradation of sugar alcohols	56.25	9 of 16
66794	lipid A biosynthesis	55.56	5 of 9
66794	lipid metabolism	54.84	17 of 31
66794	metabolism of disaccharids	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	toluene degradation	50	2 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	ribulose monophosphate pathway	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	glycogen biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	urea cycle	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	oxidative phosphorylation	45.05	41 of 91
66794	nitrate assimilation	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	vitamin B12 metabolism	41.18	14 of 34
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	ascorbate metabolism	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	starch degradation	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	daunorubicin biosynthesis	22.22	2 of 9

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
15976	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Wastewater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15976	activated sludge of an aerobic, pyrethroid-contaminated wastewater	Jiangsu province	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15976	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2596583600 annotated assembly for Sphingobium faniae CGMCC 1.7749	scaffold	GCA_900100475	570446.3	2596583600	570446	35.05

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15976	Sphingobium faniae strain JZ-2 16S ribosomal RNA gene, partial sequence	FJ373058	1401		570446

GC content

@ref	GC-content (mol%)	Method
15976	63.8±0.8	thermal denaturation, midpoint method (Tm)
29261	63.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobium faniae CGMCC 1.7749
NCBI: GCA_900100475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.00	no
125439	motility	BacteriaNetⓘ	yes	57.80	no
125439	gram_stain	BacteriaNetⓘ	negative	96.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	92.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobium faniae CGMCC 1.7749
NCBI: GCA_900100475.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.32	yes
125438	anaerobic	anaerobicⓘ	no	95.73	no
125438	aerobic	aerobicⓘ	yes	88.81	yes
125438	spore-forming	spore-formingⓘ	no	89.93	no
125438	thermophilic	thermophileⓘ	no	97.43	yes
125438	flagellated	motile2+ⓘ	yes	64.46	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Pyrethroid Carboxylesterase PytH from Sphingobium faniae JZ-2: Structure and Catalytic Mechanism.	Xu D, Gao Y, Sun B, Ran T, Zeng L, He J, He J, Wang W	Appl Environ Microbiol	10.1128/AEM.02971-19	2020
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

References

#15976	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21829
#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 )
#25679	IJSEM 408 2010 ( DOI 10.1099/ijs.0.009795-0 , PubMed 19651728 )
#29261	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25679
#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 )
#68369	Automatically annotated from API 20NE .
#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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Sphingobium faniae (DSM 21829, CGMCC 1.7749, JZ-2)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900100475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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