Name: Pseudoxanthomonas yeongjuensis GR12-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17513

Type strain:

Species: Pseudoxanthomonas yeongjuensis

Strain Designation: GR12-1

Culture col. no.: DSM 18204, CIP 109605, KACC 11580

Strain history: CIP <- 2007, DSMZ <- S.W. Kwon, KACC <- H.-Y. Weon, Suwon, Korea: strain GR12-1

NCBI tax ID(s): 377616 (species)

SI-ID 297301

DSM 18204, KACC 11580, CIP 109605

Section

Pseudoxanthomonas yeongjuensis GR12-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil cultivated with Korean ginseng.

Gram-negative
motile
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Pseudoxanthomonas*
	Species	**Pseudoxanthomonas yeongjuensis**
	Full Scientific Name (LPSN)	Pseudoxanthomonas yeongjuensis Yoo et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31821]	Gram stain	negative
[Ref.: #124016]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.946

[Ref.: #31821]	Cell length	2.15 µm

[Ref.: #31821]	Cell width	0.75 µm

[Ref.: #31821]	Cell shape	rod-shaped
[Ref.: #124016]	Cell shape	rod-shaped

[Ref.: #31821]	Motility	yes
[Ref.: #124016]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7428]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7428]

Culture medium growth

[Ref.: #7428]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7428]

Culture medium composition

expand / minimize

[Ref.: #37785]

Culture medium

MEDIUM 372 - for Aquabacterium

[Ref.: #37785]

Culture medium growth

[Ref.: #37785]

Culture medium composition

expand / minimize

[Ref.: #124016]

Culture medium

CIP Medium 372

[Ref.: #124016]

Culture medium growth

[Ref.: #124016]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7428]	growth	30 °C
[Ref.: #31821]	growth	05-33 °C
[Ref.: #31821]	optimum	28 °C
[Ref.: #37785]	growth	30 °C

[Ref.: #7428]	Temperature range	mesophilic
[Ref.: #31821]	Temperature range	mesophilic
[Ref.: #37785]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31821]			optimum	7
[Ref.: #31821]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31821]	Oxygen tolerance	aerobe
[Ref.: #124016]	Oxygen tolerance	obligate aerobe

[Ref.: #31821]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31821]		NaCl		growth	0-2	%
[Ref.: #31821]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31821]	esculin ChEBI	+	hydrolysis
[Ref.: #31821]	glucose ChEBI	+	carbon source
[Ref.: #31821]	maltose ChEBI	+	carbon source
[Ref.: #31821]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #124016]	nitrate ChEBI	-	reduction
[Ref.: #124016]	nitrite ChEBI	+	reduction

	Metabolite production	Metabolite	Production
[Ref.: #124016]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #31821]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31821]	catalase	+	1.11.1.6
[Ref.: #124016]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31821]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #31821]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #124016]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #124016]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #124016]	11993	-	+	+	+	-	+	-	-	+	+	+	+	-	-	-	-	+	-	-	-

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

[Ref.: #7428]	Sample type/isolated from	soil cultivated with Korean ginseng
[Ref.: #7428]	Country	Republic of Korea
[Ref.: #7428]	Country ISO 3 Code	KOR
[Ref.: #7428]	Continent	Asia

[Ref.: #124016]	Sample type/isolated from	Environment, Soil, ginseng
[Ref.: #124016]	Geographic location (country and/or sea, region)	Yeongju, North Gyeongsang
[Ref.: #124016]	Country	Republic of Korea
[Ref.: #124016]	Country ISO 3 Code	KOR
[Ref.: #124016]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ438977 (>99% sequence identity) for Pseudoxanthomonas from Microbeatlas

Aquatic Samples	1640
Soil Samples	2902
Animal Samples	498
Plant Samples	284
Total Samples	5324

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

[Ref.: #7428]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #124016]	Biosafety level	1	Risk group (French classification)

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.: #7428]	Pseudoxanthomonas yeongjuensis strain GR12-1 16S ribosomal RNA gene, partial sequence	DQ438977	1455	ENA	377616 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoxanthomonas yeongjuensis DSM 18204	GCA_010093345	contig	GenBank	377616 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas yeongjuensis strain DSM 18204	377616.3	wgs	PATRIC	377616 tax ID	*

[Ref.: #31821]

GC-content

63.4 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: Pseudoxanthomonas yeongjuensis strain DSM 18204 PATRIC: 377616.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoxanthomonas yeongjuensis strain DSM 18204 PATRIC: 377616.3
[Ref.: #69480]	gram-positive	no	98.027	yes
[Ref.: #69480]	anaerobic	no	99.518	yes
[Ref.: #69480]	halophile	no	96.636	yes
[Ref.: #69480]	spore-forming	no	96.684	yes
[Ref.: #69480]	glucose-util	yes	89.074	yes
[Ref.: #69480]	aerobic	yes	93.296	yes
[Ref.: #69480]	thermophile	no	98.313	no
[Ref.: #69480]	motile	no	80.826	yes
[Ref.: #69480]	flagellated	no	98.439	no
[Ref.: #69480]	glucose-ferment	no	89.041	no

Availability in culture collections External links

[Ref.: #7428]

Culture collection no.

DSM 18204, CIP 109605, KACC 11580

[Ref.: #86510]

SI-ID 297301

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 sacheonensis sp. nov., isolated from BTEX-contaminated soil in Korea, transfer of Stenotrophomonas dokdonensis Yoon et al. 2006 to the genus Pseudoxanthomonas as Pseudoxanthomonas dokdonensis comb. nov. and emended description of the genus Pseudoxanthomonas.	Lee DS, Ryu SH, Hwang HW, Kim YJ, Park M, Lee JR, Lee SS, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.65678-0	2008	*
Phylogeny	Pseudoxanthomonas yeongjuensis sp. nov., isolated from soil cultivated with Korean ginseng.	Yoo SH, Weon HY, Kim BY, Kim JH, Baek YK, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64427-0	2007	*

References

#7428

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18204

#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 )

#31821

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 #28087 (see below)

#37785 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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 )

#86510

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-ID297301.1 )

#124016 Collection of Institut Pasteur ; Curators of the CIP; CIP 109605

#28087

IJSEM 646 2007 ( DOI 10.1099/ijs.0.64427-0 , PubMed 17329800 )

* These data were automatically processed and therefore are not curated

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Pseudoxanthomonas yeongjuensis strain DSM 18204

Pseudoxanthomonas yeongjuensis strain DSM 18204

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