Sphingopyxis ginsengisoli (DSM 22237, KCTC 12582, LMG 23390)

Name: Sphingopyxis ginsengisoli (DSM 22237, KCTC 12582, LMG 23390)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24564

Type strain

Culture col. no. DSM 22237 KCTC 12582 LMG 23390 Gsoil 250

NCBI tax ID(s) 363839

Special Collections DSMZ KCTC Literature strains

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Sphingopyxis ginsengisoli DSM 22237 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from soil of a ginseng field.

Gram-negative motile rod-shaped aerobe mesophilic 16S sequence

Name and taxonomic classification

SI-ID 289687

LMG 23390,KCTC 12582,DSM 22237

@ref 20215

Last LPSN update 2025-12-16 09:52:52

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingopyxis

Species Sphingopyxis ginsengisoli

Full scientific name Sphingopyxis ginsengisoli Lee et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
31823	negative	1-1.2 µm	0.2-0.3 µm	rod-shaped
67771	negative

Pigmentation

31823

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20821	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20821	positive	growth	28	mesophilic
31823	positive	growth	04-42
31823	positive	optimum	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31823	positive	optimum	7
31823	positive	growth	5-8.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31823	aerobe
67771	aerobe

Spore formation

31823

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31823	NaCl	positive	growth	0-5 %
31823	NaCl	positive	optimum	0-5 %

Observation

31823

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31823	37054 ChEBI	3-hydroxybutyrate	+	carbon source
31823	17128 ChEBI	adipate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31823	16449 ChEBI	alanine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31823	22653 ChEBI	asparagine	+	carbon source
31823	17057 ChEBI	cellobiose	+	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
31823	16296 ChEBI	D-tryptophan	+	carbon source
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31823	33984 ChEBI	fucose	+	carbon source
31823	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31823	17234 ChEBI	glucose	+	carbon source
31823	29987 ChEBI	glutamate	+	carbon source
31823	27570 ChEBI	histidine	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
31823	24996 ChEBI	lactate	+	carbon source
31823	25017 ChEBI	leucine	+	carbon source
31823	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
31823	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
31823	26271 ChEBI	proline	+	carbon source
31823	17272 ChEBI	propionate	+	carbon source
31823	26546 ChEBI	rhamnose	+	carbon source
31823	30031 ChEBI	succinate	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
31823	31011 ChEBI	valerate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
31823	catalase	+	1.11.1.6
31823	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
20821	-	-	-	-	-	+	-	+	+	-	-	-	-	+	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
20821	soil of a ginseng field	Pocheon province	Republic of Korea	KOR	Asia
67771	From soil of the ginseng field		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB245343 (>99% sequence identity) for Sphingopyxis from Microbeatlas

Aquatic Samples	3
Soil Samples	3
Animal Samples	5
Plant Samples	1
Total Samples	12

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20821	1	Risk group (German classification)

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20821	Sphingopyxis ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 250	AB245343	1455		363839

GC content

20821

GC-content (mol%)69.2

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Diversity and antibiotic resistance patterns of Sphingomonadaceae isolates from drinking water.	Vaz-Moreira I, Nunes OC, Manaia CM.	Appl Environ Microbiol	10.1128/aem.00579-11	2011
Phylogeny	Sphingopyxis lindanitolerans sp. nov. strain WS5A3p(T) enriched from a pesticide disposal site.	Kaminski MA, Sobczak A, Spolnik G, Danikiewicz W, Dziembowski A, Lipinski L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003094	2018
Phylogeny	Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil.	Verma H, Rani P, Kumar Singh A, Kumar R, Dwivedi V, Negi V, Lal R	Int J Syst Evol Microbiol	10.1099/ijsem.0.000482	2015
Phylogeny	Sphingopyxis italica sp. nov., isolated from Roman catacombs.	Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijs.0.046573-0	2012
Phylogeny	Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field.	Srinivasan S, Kim MK, Sathiyaraj G, Veena V, Mahalakshmi M, Kalaiselvi S, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.019414-0	2009
Phylogeny	Sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.	Lee M, Ten LN, Lee HW, Oh HW, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64431-0	2008

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 )
#20821	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22237
#31823	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 #28089 (see below)
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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Sphingopyxis ginsengisoli (DSM 22237, KCTC 12582, LMG 23390)

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

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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