Name: Sphingomonas dokdonensis DS-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14247

Type strain:

Species: Sphingomonas dokdonensis

Strain Designation: DS-4

Culture col. no.: DSM 21029, CIP 108841, KCTC 12541

Strain history: CIP <- 2005, J.H. Yoon, KRIBB, Taejon, South Korea: strain DS-4

NCBI tax ID(s): 344880 (species)

SI-ID 297316

CIP 108841, KCTC 12541, DSM 21029

Other strains from Sphingomonas dokdonensis

S. dokdonensis CIP 109993

Section

Sphingomonas dokdonensis DS-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

Gram-negative
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	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas dokdonensis**
	Full Scientific Name (LPSN)	Sphingomonas dokdonensis Yoon et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #118956]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.97

[Ref.: #118956]	Cell shape	rod-shaped

[Ref.: #118956]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15517]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #15517]

Culture medium growth

[Ref.: #15517]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15517]

Culture medium composition

expand / minimize

[Ref.: #38338]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #38338]

Culture medium growth

[Ref.: #38338]

Culture medium composition

expand / minimize

[Ref.: #118956]

Culture medium

CIP Medium 72

[Ref.: #118956]

Culture medium growth

[Ref.: #118956]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15517]	growth	25 °C
[Ref.: #38338]	growth	25 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #15517]	Temperature range	mesophilic
[Ref.: #38338]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #118956]	Oxygen tolerance	obligate aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.998

	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]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #118956]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #118956]	nitrite ChEBI	-	reduction
[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.: #118956]		indole ChEBI	no
[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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118956]	alcohol dehydrogenase	-	1.1.1.1
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118956]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #118956]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118956]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118956]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118956]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #15517]	23248	-	-	-	-	-	+	+	-	+	-	+	-	-	-	-	-	+	+/-	-	-	-

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.: #118956]	11502	-	+	+	+	-	+	+	-	+	+	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #15517]	Sample type/isolated from	soil
[Ref.: #15517]	Geographic location (country and/or sea, region)	Island Dokdo
[Ref.: #15517]	Country	Republic of Korea
[Ref.: #15517]	Country ISO 3 Code	KOR
[Ref.: #15517]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #118956]	Sample type/isolated from	Environment, Soil
[Ref.: #118956]	Geographic location (country and/or sea, region)	Dokdo Island
[Ref.: #118956]	Country	Republic of Korea
[Ref.: #118956]	Country ISO 3 Code	KOR
[Ref.: #118956]	Continent	Asia
[Ref.: #118956]	Isolation date	2004
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #15517]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118956]	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.: #15517]	Sphingomonas dokdonensis strain DS-4 16S ribosomal RNA gene, partial sequence	DQ178975	1441	ENA	344880 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas dokdonensis DSM 21029	GCA_002197685	contig	GenBank	344880 tax ID	*
[Ref.: #66792]	Sphingomonas dokdonensis strain DSM 21029	344880.4	wgs	PATRIC	344880 tax ID	*
[Ref.: #66792]	Sphingomonas dokdonensis DSM 21029	2906672925	draft	JGI IMG/M	344880 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: Sphingomonas dokdonensis strain DSM 21029 PATRIC: 344880.4
[Ref.: #69481]	spore-forming	no	83	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas dokdonensis strain DSM 21029 PATRIC: 344880.4
[Ref.: #69480]	gram-positive	no	97.453	yes
[Ref.: #69480]	anaerobic	no	99.218	yes
[Ref.: #69480]	halophile	no	92.535	no
[Ref.: #69480]	spore-forming	no	96.201	no
[Ref.: #69480]	glucose-util	yes	84.241	yes
[Ref.: #69480]	motile	yes	68.278	no
[Ref.: #69480]	flagellated	no	90.502	no
[Ref.: #69480]	thermophile	no	98.808	yes
[Ref.: #69480]	aerobic	yes	93.949	yes
[Ref.: #69480]	glucose-ferment	no	92.023	no

Availability in culture collections External links

[Ref.: #15517]

Culture collection no.

DSM 21029, CIP 108841, KCTC 12541

[Ref.: #83406]

SI-ID 297316

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	*
Genetics	Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029.	Poehlein A, Wubbeler JH, Daniel R, Steinbuchel A	Genome Announc	10.1128/genomeA.00889-17	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 olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002010	2017	*
Phylogeny	Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica.	Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.003285-0	2009	*
Phylogeny	Sphingomonas sanxanigenens sp. nov., isolated from soil.	Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RL	Int J Syst Evol Microbiol	10.1099/ijs.0.000257-0	2009	*
Phylogeny	Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.	Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.64441-0	2007	*
Phylogeny	Sphingomonas dokdonensis sp. nov., isolated from soil.	Yoon JH, Lee MH, Kang SJ, Lee SY, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64114-0	2006	*

References

#15517

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21029

#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 )

#38338 ; 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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#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 )

#83406

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-ID297316.1 )

#118956 Collection of Institut Pasteur ; Curators of the CIP; CIP 108841
* These data were automatically processed and therefore are not curated

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Sphingomonas dokdonensis strain DSM 21029

Sphingomonas dokdonensis strain DSM 21029

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