Sphingobacterium wenxiniae (DSM 22789, ACCC 05410, CCTCC AB 2010005)

Name: Sphingobacterium wenxiniae (DSM 22789, ACCC 05410, CCTCC AB 2010005)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14129

Type strain

Strain Designation LQY-18

Culture col. no. DSM 22789 ACCC 05410 CCTCC AB 2010005 KCTC 23009 LQY-18

NCBI tax ID(s) 683125

Special Collections DSMZ KCTC Literature strains

History <- J. Zhang, Nanjing Agric. Univ., China; LQY-18

Links

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

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

Name and taxonomic classification

SI-ID 402443

KCTC 23009,DSM 22789

@ref 20215

Last LPSN update 2026-02-09 11:21:20

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Sphingobacterium

Species Sphingobacterium wenxiniae

Full scientific name Sphingobacterium wenxiniae Zhang et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30307	negative	0.6-1.4 µm	0.3-0.6 µm	rod-shaped
125438	negative				98.604
125439	negative				99.4

Pigmentation

30307

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16519	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16519	positive	growth	28
30307	positive	growth	08-40
30307	positive	optimum	30

Culture pH

@ref	Ability	Type	PH	PH range
30307	positive	optimum	07-08
30307	positive	growth	05-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

30307

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
30307
125438		92.331
125439		98.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30307	NaCl	positive	growth	0-5 %
30307	NaCl	positive	optimum	1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30307	4853 ChEBI	esculin	+	hydrolysis
30307	33984 ChEBI	fucose	+	carbon source
30307	28087 ChEBI	glycogen	+	carbon source
30307	26271 ChEBI	proline	+	carbon source
30307	27082 ChEBI	trehalose	+	carbon source
30307	53424 ChEBI	tween 20	+	carbon source
30307	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30307	acid phosphatase	+	3.1.3.2
30307	alkaline phosphatase	+	3.1.3.1
30307	alpha-galactosidase	+	3.2.1.22
30307	catalase	+	1.11.1.6
30307	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	-
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Industrial wastewater
#Engineered	#Waste	#Water treatment plant

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16519	activated sludge of a wastewater treatment plant in a synthetic pyrethroid-manufacturing facility	Jiangsu Province, Yangzhou	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16519	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 2634166295 annotated assembly for Sphingobacterium wenxiniae DSM 22789	scaffold	GCA_900116225	683125.3	2634166295	683125	69.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16519	Sphingobacterium wenxiniae strain LQY-18 16S ribosomal RNA gene, partial sequence	GQ988781	1453		683125

GC content

@ref	GC-content (mol%)	Method
16519	40.3	thermal denaturation, midpoint method (Tm)
30307	40.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobacterium wenxiniae DSM 22789
NCBI: GCA_900116225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.30	no
125439	motility	BacteriaNetⓘ	no	51.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	76.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobacterium wenxiniae DSM 22789
NCBI: GCA_900116225.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.60	yes
125438	anaerobic	anaerobicⓘ	no	95.52	no
125438	aerobic	aerobicⓘ	yes	82.49	yes
125438	spore-forming	spore-formingⓘ	no	92.33	no
125438	thermophilic	thermophileⓘ	no	97.63	yes
125438	flagellated	motile2+ⓘ	no	85.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
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

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 )
#26648	IJSEM 683 2012 ( DOI 10.1099/ijs.0.033118-0 , PubMed 21551333 )
#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
#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 .
#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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Sphingobacterium wenxiniae (DSM 22789, ACCC 05410, CCTCC AB 2010005)

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

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900116225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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