Name: Sphingomonas kyeonggiensis THG-DT81
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131288

Type strain:

Species: Sphingomonas kyeonggiensis

Strain Designation: THG-DT81

Culture col. no.: DSM 101806, JCM 18825, KACC 17173

Strain history: T.-H. Yi THG-DT81.

NCBI tax ID(s): 1268553 (species)

SI-ID 407861

DSM 101806

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Sphingomonas kyeonggiensis THG-DT81 is a mesophilic, Gram-negative bacterium that was isolated from soil of a ginseng field.

Gram-negative
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas kyeonggiensis**
	Full Scientific Name (LPSN)	Sphingomonas kyeonggiensis corrig. Son et al. 2014

Synonym

Sphingomonas kyeonggiense

Information on morphological and physiological properties Morphology

[Ref.: #125438]	Gram stain	negative Confidence in %95.5
[Ref.: #125439]	Gram stain	negative Confidence in %97

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22515]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #22515]

Culture medium growth

[Ref.: #22515]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22515]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22515]			growth	28 °C
[Ref.: #67770]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %93

[Ref.: #125439]

Ability of spore formation

no Confidence in %94.9

[Ref.: #67770]

Observation

quinones: Q-10

	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]	maltose 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.: #22515]	26234	-	-	-	-	-	+	-	+	+	+	+	-	+	+	-	-	-	+	-	-	-

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

[Ref.: #22515]	Sample type/isolated from	soil of a ginseng field
[Ref.: #22515]	Geographic location (country and/or sea, region)	Pocheon Province
[Ref.: #22515]	Country	Republic of Korea
[Ref.: #22515]	Country ISO 3 Code	KOR
[Ref.: #22515]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of ginseng field of Pocheon Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	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?

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

[Ref.: #22515]

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.: #22515]	Sphingomonas kyeonggiensis strain THG-DT81 16S ribosomal RNA gene, partial sequence	KC252615	1407	GenBank ENA	1268553 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas kyeonggiensis DSM 101806	GCA_014196745	scaffold	GenBank ENA	1268553 tax ID	*
[Ref.: #66792]	Sphingomonas kyeonggiensis strain DSM 101806	1268553.3	wgs	PATRIC	1268553 tax ID	*
[Ref.: #66792]	Sphingomonas kyeonggiensis DSM 101806	2829979998	draft	JGI IMG/M	1268553 tax ID	*

[Ref.: #67770]

GC-content

66.8 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas kyeonggiensis DSM 101806 NCBI: GCA_014196745.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	95.5	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	93.032	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	89.128	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	88.195	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.077	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	73.864	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas kyeonggiensis DSM 101806 NCBI: GCA_014196745
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	93
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	74.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	94.9

Availability in culture collections External links

[Ref.: #22515]

Culture collection no.

DSM 101806, JCM 18825, KACC 17173

[Ref.: #89730]

SI-ID 407861

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas flavalba sp. nov., isolated from a procymidone-contaminated soil.	Zhou XY, Zhang L, Su XJ, Hang P, Hu B, Jiang JD	Int J Syst Evol Microbiol	10.1099/ijsem.0.003581	2019	*
Phylogeny	Sphingomonas antarctica sp. nov., isolated from Antarctic tundra soil.	Huang Y, Wei Z, Danzeng W, Kim MC, Zhu G, Zhang Y, Liu Z, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.002253	2017	*
Phylogeny	Sphingomonas silvisoli sp. nov., isolated from forest soil.	Ko Y, Hwang WM, Kim M, Kang K, Ahn TY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002001	2017	*
Phylogeny	Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum.	Zhu L, Si M, Li C, Xin K, Chen C, Shi X, Huang R, Zhao L, Shen X, Zhang L	Int J Syst Evol Microbiol	10.1099/ijs.0.000074	2015	*
Phylogeny	Sphingomonas kyeonggiense sp. nov., isolated from soil of a ginseng field.	Son HM, Kook M, Tran HT, Kim KY, Park SY, Kim JH, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0122-7	2014	*
Phylogeny	Sphingomonas psychrotolerans sp. nov., isolated from root surface of Leontopodium leontopodioides in the Tianshan Mountains, Xinjiang, China.	Luo Y, Zhou M, Wang F, Sheng H	Int J Syst Evol Microbiol	10.1099/ijsem.0.005396	2022	*
Phylogeny	Sphingomonas carri sp. nov., isolated from a car air-conditioning system.	Lee H, Kim DU, Lee S, Yun J, Park S, Yoon JH, Park SY, Ka JO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002250	2017	*
Phylogeny	Sphingomonas frigidaeris sp. nov., isolated from an air conditioning system.	Lee Y, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002221	2017	*

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 )

#22515

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101806

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68369

Automatically annotated from API 20NE .

#89730

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-ID407861.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Sphingomonas kyeonggiensis DSM 101806

Sphingomonas kyeonggiensis DSM 101806

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