Name: Sphingopyxis ginsengisoli DSM 22237
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24564

Type strain:

Species: Sphingopyxis ginsengisoli

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

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 363839 (species)

SI-ID 289687

LMG 23390, KCTC 12582, DSM 22237

Section

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

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

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	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingopyxis*
	Species	**Sphingopyxis ginsengisoli**
	Full Scientific Name (LPSN)	Sphingopyxis ginsengisoli Lee et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #31823]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #31823]	Cell length	1-1.2 µm

[Ref.: #31823]	Cell width	0.2-0.3 µm

[Ref.: #31823]	Cell shape	rod-shaped

[Ref.: #31823]	Motility	yes

[Ref.: #31823]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20821]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #20821]

Culture medium growth

[Ref.: #20821]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20821]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20821]	growth	28 °C
[Ref.: #31823]	growth	04-42 °C
[Ref.: #31823]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #20821]	Temperature range	mesophilic
[Ref.: #31823]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31823]			optimum	7
[Ref.: #31823]			growth	5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31823]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31823]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31823]		NaCl		growth	0-5	%
[Ref.: #31823]		NaCl		optimum	0-5	%

[Ref.: #31823]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31823]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #31823]	adipate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31823]	alanine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31823]	asparagine ChEBI	+	carbon source
[Ref.: #31823]	cellobiose ChEBI	+	carbon source
[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.: #31823]	D-tryptophan ChEBI	+	carbon source
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #31823]	fucose ChEBI	+	carbon source
[Ref.: #31823]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31823]	glucose ChEBI	+	carbon source
[Ref.: #31823]	glutamate ChEBI	+	carbon source
[Ref.: #31823]	histidine ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #31823]	lactate ChEBI	+	carbon source
[Ref.: #31823]	leucine ChEBI	+	carbon source
[Ref.: #31823]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #31823]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #31823]	proline ChEBI	+	carbon source
[Ref.: #31823]	propionate ChEBI	+	carbon source
[Ref.: #31823]	rhamnose ChEBI	+	carbon source
[Ref.: #31823]	succinate ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31823]	valerate ChEBI	+	carbon source
	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.: #31823]	catalase	+	1.11.1.6
[Ref.: #31823]	cytochrome oxidase	+	1.9.3.1
[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.: #20821]	23257	-	-	-	-	-	+	-	+	+	-	-	-	-	+	-	-	-	+	-	-	+

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

[Ref.: #20821]	Sample type/isolated from	soil of a ginseng field
[Ref.: #20821]	Geographic location (country and/or sea, region)	Pocheon province
[Ref.: #20821]	Country	Republic of Korea
[Ref.: #20821]	Country ISO 3 Code	KOR
[Ref.: #20821]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil of the ginseng field
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #20821]

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.: #20821]	Sphingopyxis ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 250	AB245343	1455	ENA	363839 tax ID

[Ref.: #20821]

GC-content

69.2 mol%

Availability in culture collections External links

[Ref.: #20821]

Culture collection no.

DSM 22237, KCTC 12582, LMG 23390, Gsoil 250

[Ref.: #88418]

SI-ID 289687

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#88418

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-ID289687.1 )

#28089

IJSEM 2342 2008 ( DOI 10.1099/ijs.0.64431-0 , PubMed 18842853 )

* These data were automatically processed and therefore are not curated

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