Name: Sphingobacterium wenxiniae LQY-18
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14129

Type strain:

Species: Sphingobacterium wenxiniae

Strain Designation: LQY-18

Culture col. no.: DSM 22789, ACCC 05410, CCTCC AB 2010005, KCTC 23009

Strain history: <- J. Zhang, Nanjing Agric. Univ., China; LQY-18

NCBI tax ID(s): 683125 (species)

SI-ID 402443

DSM 22789

Section

Sphingobacterium wenxiniae LQY-18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge of a wastewater treatment plant in a synthetic pyrethroid-manufacturing facility.

Gram-negative
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	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Sphingobacterium*
	Species	**Sphingobacterium wenxiniae**
	Full Scientific Name (LPSN)	Sphingobacterium wenxiniae Zhang et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30307]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #30307]	Cell length	0.6-1.4 µm

[Ref.: #30307]	Cell width	0.3-0.6 µm

[Ref.: #30307]	Cell shape	rod-shaped

[Ref.: #30307]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.09

[Ref.: #30307]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16519]

Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

[Ref.: #16519]

Culture medium growth

[Ref.: #16519]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16519]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16519]	growth	28 °C
[Ref.: #30307]	growth	08-40 °C
[Ref.: #30307]	optimum	30 °C

[Ref.: #16519]	Temperature range	mesophilic
[Ref.: #30307]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30307]			optimum	07-08
[Ref.: #30307]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30307]

Oxygen tolerance

aerobe

[Ref.: #30307]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30307]		NaCl		growth	0-5	%
[Ref.: #30307]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30307]	esculin ChEBI	+	hydrolysis
[Ref.: #30307]	fucose ChEBI	+	carbon source
[Ref.: #30307]	glycogen ChEBI	+	carbon source
[Ref.: #30307]	proline ChEBI	+	carbon source
[Ref.: #30307]	trehalose ChEBI	+	carbon source
[Ref.: #30307]	tween 20 ChEBI	+	carbon source
[Ref.: #30307]	tween 80 ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30307]	acid phosphatase	+	3.1.3.2
[Ref.: #30307]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30307]	alpha-galactosidase	+	3.2.1.22
[Ref.: #30307]	catalase	+	1.11.1.6
[Ref.: #30307]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	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.: #16519]	Sample type/isolated from	activated sludge of a wastewater treatment plant in a synthetic pyrethroid-manufacturing facility
[Ref.: #16519]	Geographic location (country and/or sea, region)	Jiangsu Province, Yangzhou
[Ref.: #16519]	Country	China
[Ref.: #16519]	Country ISO 3 Code	CHN
[Ref.: #16519]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Industrial wastewater
#Engineered	#Waste	#Water treatment plant

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ988781 (>99% sequence identity) for Sphingobacterium wenxiniae subclade from Microbeatlas

Aquatic Samples	226
Soil Samples	270
Animal Samples	682
Plant Samples	86
Total Samples	1264

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

[Ref.: #16519]

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.: #16519]	Sphingobacterium wenxiniae strain LQY-18 16S ribosomal RNA gene, partial sequence	GQ988781	1453	ENA	683125 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobacterium wenxiniae DSM 22789	GCA_900116225	scaffold	GenBank	683125 tax ID	*
[Ref.: #66792]	Sphingobacterium wenxiniae strain DSM 22789	683125.3	wgs	PATRIC	683125 tax ID	*
[Ref.: #66792]	Sphingobacterium wenxiniae DSM 22789	2634166295	draft	JGI IMG/M	683125 tax ID	*

[Ref.: #16519]	GC-content	40.3 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #30307]	GC-content	40.3 mol%

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: Sphingobacterium wenxiniae DSM 22789 NCBI: GCA_900116225.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobacterium wenxiniae DSM 22789 NCBI: GCA_900116225.1
[Ref.: #69480]	motile	no	92.828	yes
[Ref.: #69480]	flagellated	no	95.324	yes
[Ref.: #69480]	gram-positive	no	98.355	no
[Ref.: #69480]	anaerobic	no	98.929	no
[Ref.: #69480]	aerobic	yes	89.773	yes
[Ref.: #69480]	halophile	no	91.898	yes
[Ref.: #69480]	spore-forming	no	96.301	no
[Ref.: #69480]	glucose-ferment	no	91.001	no
[Ref.: #69480]	thermophile	no	99.121	yes
[Ref.: #69480]	glucose-util	yes	88.71	no

Availability in culture collections External links

[Ref.: #16519]

Culture collection no.

DSM 22789, ACCC 05410, CCTCC AB 2010005, KCTC 23009

[Ref.: #83294]

SI-ID 402443

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata.	Sun JQ, Liu M, Wang XY, Xu L, Wu XL	Int J Syst Evol Microbiol	10.1099/ijsem.0.000600	2015	*
Phylogeny	Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge.	Zhang J, Zheng JW, Cho BC, Hwang CY, Fang C, He J, Li SP	Int J Syst Evol Microbiol	10.1099/ijs.0.033118-0	2011	*
	Organoarsenical tolerance in Sphingobacterium wenxiniae, a bacterium isolated from activated sludge.	Chen J, Zhang J, Rosen BP	Environ Microbiol	10.1111/1462-2920.15599	2021	*

References

#16519

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22789

#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 )

#30307

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 #26648 (see below)

#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 )

#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 )

#83294

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-ID402443.1 )

#26648

IJSEM 683 2012 ( DOI 10.1099/ijs.0.033118-0 , PubMed 21551333 )

* These data were automatically processed and therefore are not curated

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Sphingobacterium wenxiniae DSM 22789

Sphingobacterium wenxiniae DSM 22789

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