Name: Sphingorhabdus wooponensis 03SU3-P
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 130685

Type strain:

Species: Sphingorhabdus wooponensis

Strain Designation: 03SU3-P

Culture col. no.: DSM 29350, JCM 17547, KCTC 23340

Strain history: C. N. Seong 03SU3-P.

NCBI tax ID(s): 940136 (species)

SI-ID 405404

DSM 29350

Special Collections

Section

Sphingorhabdus wooponensis 03SU3-P is a bacterium that was isolated from wetland freshwater.

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	*Sphingorhabdus*
	Species	**Sphingorhabdus wooponensis**
	Full Scientific Name (LPSN)	Sphingorhabdus wooponensis (Baik et al. 2013) Park et al. 2014

Synonym

Sphingopyxis wooponensis

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #21796]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21796]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21796]			growth	25 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[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.: #21796]	23293	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+

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

[Ref.: #21796]	Sample type/isolated from	wetland freshwater
[Ref.: #21796]	Geographic location (country and/or sea, region)	Woopo wetland
[Ref.: #21796]	Country	Republic of Korea
[Ref.: #21796]	Country ISO 3 Code	KOR
[Ref.: #21796]	Continent	Asia
[Ref.: #21796]	Geographic location	35.5500°/128.4170°

[Ref.: #67770]	Sample type/isolated from	Freshwater of Woopo wetland (35° 33' N 128° 25' E) in Gyeongnam Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
[Ref.: #67770]	Geographic location	35.5500°/128.4170°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Terrestrial	#Wetland (Swamp)

What are isolation sources categories?

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Global distribution of 16S sequence HQ436493 (>99% sequence identity) for Sphingorhabdus wooponensis from Microbeatlas

Aquatic Samples	7836
Soil Samples	1099
Animal Samples	697
Plant Samples	418
Total Samples	10050

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

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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.: #21796]	Sphingopyxis wooponensis strain 03SU3-P 16S ribosomal RNA gene, partial sequence	HQ436493	1435	GenBank ENA	940136 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Sphingorhabdus wooponensis 03SU3-P	GCA_003933235	contig	GenBank ENA	940136 tax ID
[Ref.: #66792]	Sphingorhabdus wooponensis 03SU3-P	2891008005	draft	JGI IMG/M	940136 tax ID	*

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GC-content

53.3 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #21796]

Culture collection no.

DSM 29350, JCM 17547, KCTC 23340

[Ref.: #89192]

SI-ID 405404

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis.	Baik KS, Choe HN, Park SC, Hwang YM, Kim EM, Park C, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.044057-0	2012	*
Phylogeny	Sphingorhabdus pulchriflava sp. nov., isolated from a river.	Jung GY, Nam IH, Han YS, Ahn JS, Rhee SK, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003503	2019	*
Phylogeny	Sphingopyxis contaminans sp. nov., isolated from a contaminated Petri dish.	Subhash Y, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.061937-0	2014	*

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 )

#21796

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29350

#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 .

#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 .

#89192

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-ID405404.1 )

* These data were automatically processed and therefore are not curated

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