Name: Pseudoxanthomonas wuyuanensis XC21-2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130781

Type strain:

Species: Pseudoxanthomonas wuyuanensis

Strain Designation: XC21-2

Culture col. no.: DSM 100640, CGMCC 1.10978, KCTC 23877

Strain history: <- KCTC

NCBI tax ID(s): 1073196 (species)

SI-ID 397780

DSM 100640

Section

Pseudoxanthomonas wuyuanensis XC21-2 is a mesophilic, motile bacterium that was isolated from saline-alkaline soil, sunflower field.

motile
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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Pseudoxanthomonas*
	Species	**Pseudoxanthomonas wuyuanensis**
	Full Scientific Name (LPSN)	Pseudoxanthomonas wuyuanensis Li et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #69480]	Motility	yes Confidence in %92.826

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21741]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #21741]

Culture medium growth

[Ref.: #21741]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21741]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21741]			growth	37 °C

[Ref.: #21741]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

	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]	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.: #21741]	23423	+	-	-	-	-	+	+	+	+	+	+	-	+	+/-	-	-	-	+	-	-	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	oxidative phosphorylation	52.75	48 of 91
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[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]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		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.: #21741]	Sample type/isolated from	saline-alkaline soil, sunflower field
[Ref.: #21741]	Geographic location (country and/or sea, region)	Wuyuan county, Inner Mongolia
[Ref.: #21741]	Country	China
[Ref.: #21741]	Country ISO 3 Code	CHN
[Ref.: #21741]	Continent	Asia
[Ref.: #21741]	Geographic location	40.7750°/107.6030°
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Condition	#Alkaline	-
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN247803 (>99% sequence identity) for Pseudoxanthomonas from Microbeatlas

Aquatic Samples	377
Soil Samples	1714
Animal Samples	331
Plant Samples	689
Total Samples	3111

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

[Ref.: #21741]

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.: #21741]	Pseudoxanthomonas wuyuanensis 16S ribosomal RNA gene, partial sequence	JN247803	1426	ENA	1073196 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoxanthomonas wuyuanensis CGMCC 1.10978	GCA_900215535	scaffold	GenBank	1073196 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas wuyuanensis DSM 100640	GCA_010093325	contig	GenBank	1073196 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas wuyuanensis strain CGMCC 1.10978	1073196.3	wgs	PATRIC	1073196 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas wuyuanensis strain DSM 100640	1073196.4	wgs	PATRIC	1073196 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas wuyuanensis CGMCC 1.10978	2718217650	draft	JGI IMG/M	1073196 tax ID	*

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: Pseudoxanthomonas wuyuanensis CGMCC 1.10978 NCBI: GCA_900215535.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoxanthomonas wuyuanensis CGMCC 1.10978 NCBI: GCA_900215535.1
[Ref.: #69480]	flagellated	no	75.49	no
[Ref.: #69480]	gram-positive	no	98.706	no
[Ref.: #69480]	anaerobic	no	98.754	no
[Ref.: #69480]	aerobic	yes	94.415	no
[Ref.: #69480]	halophile	no	95.336	no
[Ref.: #69480]	spore-forming	no	96.033	no
[Ref.: #69480]	thermophile	no	98.745	no
[Ref.: #69480]	glucose-util	yes	89.359	yes
[Ref.: #69480]	motile	yes	84.857	no
[Ref.: #69480]	glucose-ferment	no	89.354	no

Availability in culture collections External links

[Ref.: #21741]

Culture collection no.

DSM 100640, CGMCC 1.10978, KCTC 23877

[Ref.: #89277]

SI-ID 397780

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoxanthomonas humi sp. nov., a bacterium isolated from rhizospheric soil of Fraxinus chinensis in Gyeonggi Province, South Korea.	Akter S, Jo H, Du J, Won K, Yin CS, Kook M, Yu H, Choi HS, Kim MK, Yi TH	Arch Microbiol	10.1007/s00203-015-1157-5	2015	*
Phylogeny	Pseudoxanthomonas wuyuanensis sp. nov., isolated from saline-alkali soil.	Li D, Pang H, Sun L, Fan J, Li Y, Zhang J	Int J Syst Evol Microbiol	10.1099/ijs.0.056796-0	2013	*

References

#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 )

#21741

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100640

#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 .

#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 )

#89277

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-ID397780.1 )

* These data were automatically processed and therefore are not curated

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Pseudoxanthomonas wuyuanensis CGMCC 1.10978

Pseudoxanthomonas wuyuanensis CGMCC 1.10978

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