Name: Sphingobium wenxiniae JZ-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14198

Type strain:

Species: Sphingobium wenxiniae

Strain Designation: JZ-1

Culture col. no.: DSM 21828, CGMCC 1.7748

Strain history: <- B.-Z. Wang, Nanjing Agric. Univ., China; JZ-1

NCBI tax ID(s): 595605 (species)

SI-ID 402371

DSM 21828

Section

Sphingobium wenxiniae JZ-1 is a mesophilic, Gram-negative bacterium that was isolated from activated sludge of a synthetic pyrethroid-manufacturing wastewater treatment facility.

Gram-negative
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 wenxiniae**
	Full Scientific Name (LPSN)	Sphingobium wenxiniae Wang et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.989

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15975]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15975]

Culture medium growth

[Ref.: #15975]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15975]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15975]			growth	30 °C

[Ref.: #15975]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.997

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[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.: #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.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[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.

	Metabolite production	Metabolite	Production
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

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.: #15975]	23255	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #15975]	Sample type/isolated from	activated sludge of a synthetic pyrethroid-manufacturing wastewater treatment facility
[Ref.: #15975]	Geographic location (country and/or sea, region)	Jiangsu province
[Ref.: #15975]	Country	China
[Ref.: #15975]	Country ISO 3 Code	CHN
[Ref.: #15975]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Industrial wastewater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ686047 (>99% sequence identity) for Sphingobium from Microbeatlas

Aquatic Samples	30
Soil Samples	53
Animal Samples	18
Plant Samples	145
Total Samples	246

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

[Ref.: #15975]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #15975]	Sphingobium wenxiniae strain JZ-1 16S ribosomal RNA gene, partial sequence	FJ686047	1410	ENA	595605 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium wenxiniae CGMCC 1.7748	GCA_007830065	scaffold	GenBank	595605 tax ID	*
[Ref.: #66792]	Sphingobium wenxiniae JZ-1	GCA_014205735	scaffold	GenBank	595605 tax ID	*
[Ref.: #66792]	Sphingobium wenxiniae strain CGMCC 1.7748	595605.4	wgs	PATRIC	595605 tax ID	*
[Ref.: #66792]	Sphingobium wenxiniae DSM 21828	2828337626	draft	JGI IMG/M	595605 tax ID	*
[Ref.: #66792]	Sphingobium wenxiniae CGMCC 1.7748	2596583555	draft	JGI IMG/M	595605 tax ID	*

[Ref.: #15975]

GC-content

64.2 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sphingobium wenxiniae CGMCC 1.7748 NCBI: GCA_007830065.1
[Ref.: #69481]	spore-forming	no	89	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium wenxiniae CGMCC 1.7748 NCBI: GCA_007830065.1
[Ref.: #69480]	flagellated	no	85.72	no
[Ref.: #69480]	gram-positive	no	96.83	no
[Ref.: #69480]	anaerobic	no	98.391	no
[Ref.: #69480]	aerobic	yes	90.354	no
[Ref.: #69480]	halophile	no	94.293	no
[Ref.: #69480]	spore-forming	no	93.939	no
[Ref.: #69480]	thermophile	no	95.647	no
[Ref.: #69480]	glucose-util	yes	73.834	no
[Ref.: #69480]	motile	yes	56.038	no
[Ref.: #69480]	glucose-ferment	no	92.936	yes

Availability in culture collections External links

[Ref.: #15975]

Culture collection no.

DSM 21828, CGMCC 1.7748

[Ref.: #83357]

SI-ID 402371

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	PbaR, an IclR family transcriptional activator for the regulation of the 3-phenoxybenzoate 1',2'-dioxygenase gene cluster in Sphingobium wenxiniae JZ-1T.	Cheng M, Chen K, Guo S, Huang X, He J, Li S, Jiang J	Appl Environ Microbiol	10.1128/AEM.02122-15	2015	*
Metabolism	A novel angular dioxygenase gene cluster encoding 3-phenoxybenzoate 1',2'-dioxygenase in Sphingobium wenxiniae JZ-1.	Wang C, Chen Q, Wang R, Shi C, Yan X, He J, Hong Q, Li S	Appl Environ Microbiol	10.1128/AEM.00208-14	2014	*
Phylogeny	Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site.	Kaur J, Moskalikova H, Niharika N, Sedlackova M, Hampl A, Damborsky J, Prokop Z, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.039834-0	2012	*
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	*

References

#15975

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21828

#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 )

#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) .

#68369

Automatically annotated from API 20NE .

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#83357

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-ID402371.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Sphingobium wenxiniae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Sphingobium wenxiniae CGMCC 1.7748

Sphingobium wenxiniae CGMCC 1.7748

Change proposal

Change proposal