Name: Sphingomonas ginsengisoli DSM 18094
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23277

Type strain:

Species: Sphingomonas ginsengisoli

Culture col. no.: DSM 18094, KCTC 12630, LMG 23739, Gsoil 634

Strain history: <- S.-T. Lee, KAIST, Korean Advanced Institute of Science and Technology; Gsoil 634

NCBI tax ID(s): 363835 (species)

SI-ID 401817

DSM 18094

Section

Sphingomonas ginsengisoli DSM 18094 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.

Gram-negative
rod-shaped
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 ginsengisoli**
	Full Scientific Name (LPSN)	Sphingomonas ginsengisoli An et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30596]	Gram stain	negative

[Ref.: #30596]	Cell length	1.3 µm

[Ref.: #30596]	Cell width	0.5 µm

[Ref.: #30596]	Cell shape	rod-shaped

[Ref.: #30596]	Motility	no

[Ref.: #30596]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18850]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #18850]

Culture medium growth

[Ref.: #18850]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18850]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #18850]			growth	28 °C
[Ref.: #30596]			optimum	30 °C

[Ref.: #18850]	Temperature range	mesophilic
[Ref.: #30596]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30596]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30596]

Oxygen tolerance

aerobe

[Ref.: #30596]

Ability of spore formation

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30596]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #30596]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #30596]	esculin ChEBI	+	hydrolysis
[Ref.: #30596]	glucose ChEBI	+	carbon source
[Ref.: #30596]	glycogen ChEBI	+	carbon source
[Ref.: #30596]	histidine ChEBI	+	carbon source
[Ref.: #30596]	maltose ChEBI	+	carbon source
[Ref.: #30596]	proline ChEBI	+	carbon source
[Ref.: #30596]	serine ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30596]		acid phosphatase	+	3.1.3.2
[Ref.: #30596]		gelatinase	+

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

[Ref.: #18850]	Sample type/isolated from	soil of ginseng field
[Ref.: #18850]	Geographic location (country and/or sea, region)	Pocheon province
[Ref.: #18850]	Country	Republic of Korea
[Ref.: #18850]	Country ISO 3 Code	KOR
[Ref.: #18850]	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.: #18850]

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.: #18850]	Sphingomonas ginsengisoli gene for 16S rRNA, partial sequence	AB245347	1436	ENA	363835 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	'Sphingomonas ginsengisoli' Hoang et al. 2012 KCTC 12630	GCA_003332855	contig	GenBank	1706000 tax ID	*
[Ref.: #66792]	'Sphingomonas ginsengisoli' Hoang et al. 2012 strain KCTC 12630	1706000.3	wgs	PATRIC	1706000 tax ID	*
[Ref.: #66792]	Sphingomonas ginsengisoli KCTC 12630	2874729722	draft	JGI IMG/M	1706000 tax ID	*

[Ref.: #18850]	GC-content	66.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30596]	GC-content	66.8 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: 'Sphingomonas ginsengisoli' Hoang et al. 2012 strain KCTC 12630 PATRIC: 1706000.3
[Ref.: #69480]	motile	no	79.337	yes
[Ref.: #69480]	gram-positive	no	96.793	yes
[Ref.: #69480]	anaerobic	no	99.289	yes
[Ref.: #69480]	aerobic	yes	93.31	yes
[Ref.: #69480]	halophile	no	91.972	no
[Ref.: #69480]	spore-forming	no	97.168	no
[Ref.: #69480]	thermophile	no	95.692	yes
[Ref.: #69480]	glucose-util	yes	84.527	yes
[Ref.: #69480]	flagellated	no	97.594	no
[Ref.: #69480]	glucose-ferment	no	91.536	no

Availability in culture collections External links

[Ref.: #18850]

Culture collection no.

DSM 18094, KCTC 12630, LMG 23739, Gsoil 634

[Ref.: #87499]

SI-ID 401817

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas rhizophila sp. nov., isolated from rhizosphere of Hibiscus syriacus.	Yan ZF, Lin P, Won KH, Li CT, Park G, Chin B, Kook M, Wang QJ, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002566	2018	*
Phylogeny	Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond.	Kim JH, Kim SH, Kim KH, Lee PC	Int J Syst Evol Microbiol	10.1099/ijs.0.000337	2015	*
Phylogeny	Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov.	An DS, Liu QM, Lee HG, Jung MS, Kim SC, Lee ST, Im WT	Int J Syst Evol Microbiol	10.1099/ijs.0.039578-0	2012	*
Genetics	Draft Genome Sequence of KCTC 12630, the Type Strain of the Novel Species Sphingomonas ginsengisoli.	Li YQ, Zhang H, Narsing Rao MP, Dong ZY, Alkhalifah DHM, Hozzein WN, Xiao M, Li WJ	Microbiol Resour Announc	10.1128/MRA.01032-18	2019	*
Phylogeny	Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir.	Huy H, Jin L, Lee KC, Kim SG, Lee JS, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijs.0.054510-0	2014	*

References

#18850

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18094

#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 )

#30596

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 #26927 (see below)

#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) .

#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) .

#87499

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-ID401817.1 )

#26927

IJSEM 496 2013 ( DOI 10.1099/ijs.0.039578-0 , PubMed 22505600 )

* These data were automatically processed and therefore are not curated

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'Sphingomonas ginsengisoli' Hoang et al. 2012 strain KCTC 12630

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