Sphingomonas ginsengisoli (DSM 18094, KCTC 12630, LMG 23739)

Name: Sphingomonas ginsengisoli (DSM 18094, KCTC 12630, LMG 23739)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23277

Type strain

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

NCBI tax ID(s) 363835

Special Collections DSMZ KCTC Literature strains

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

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 401817

LMG 23739,KCTC 12630,DSM 18094

@ref 20215

Last LPSN update 2025-12-16 09:52:37

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas ginsengisoli

Full scientific name Sphingomonas ginsengisoli An et al. 2013

Synonyms (1)

Pseudosphingomonas ginsengisoli

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
30596	negative	1.3 µm	0.5 µm	rod-shaped
125438	negative
125439	negative

Pigmentation

30596

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18850	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
18850	positive	growth	28	mesophilic
30596	positive	optimum	30	mesophilic

Culture pH

@ref	Ability	Type	PH
30596	positive	optimum	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30596	aerobe
125439	aerobe

Spore formation

@ref	Spore formation
30596
125439

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30596	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
30596	58143 ChEBI	5-dehydro-D-gluconate	+	carbon source
30596	4853 ChEBI	esculin	+	hydrolysis
30596	17234 ChEBI	glucose	+	carbon source
30596	28087 ChEBI	glycogen	+	carbon source
30596	27570 ChEBI	histidine	+	carbon source
30596	17306 ChEBI	maltose	+	carbon source
30596	26271 ChEBI	proline	+	carbon source
30596	17822 ChEBI	serine	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30596	acid phosphatase	+	3.1.3.2
30596	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
18850	soil of ginseng field	Pocheon province	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18850	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM333285v1 assembly for Sphingomonas sediminicola KCTC 12630	contig	GCA_003332855	1706000.3	2874729722	1706000	74.82

Genome browser: GCA_003332855

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18850	Sphingomonas ginsengisoli An et al. 2013 gene for 16S rRNA, partial sequence	AB245347	1436		363835

GC content

@ref	GC-content (mol%)	Method
18850	66.8	high performance liquid chromatography (HPLC)
30596	66.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: 'Sphingomonas ginsengisoli' Hoang et al. 2012 KCTC 12630
NCBI: GCA_003332855

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.70	no
125439	motility	BacteriaNetⓘ	yes	70.50	no
125439	gram_stain	BacteriaNetⓘ	negative	97.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: 'Sphingomonas ginsengisoli' Hoang et al. 2012 strain KCTC 12630
PATRIC: 1706000.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.75	yes
125438	anaerobic	anaerobicⓘ	no	96.80	no
125438	spore-forming	spore-formingⓘ	no	87.60	yes
125438	aerobic	aerobicⓘ	yes	87.21	no
125438	thermophilic	thermophileⓘ	no	95.95	yes
125438	flagellated	motile2+ⓘ	no	53.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.	Abe T, Akazawa Y, Toyoda A, Niki H, Baba T.	Front Microbiol	10.3389/fmicb.2020.01486	2020
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 flavus sp. nov. isolated from road soil.	Du J, Singh H, Won K, Yang JE, Akter S, Jin FX, Yi TH.	Arch Microbiol	10.1007/s00203-015-1123-2	2015
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
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) .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Sphingomonas ginsengisoli (DSM 18094, KCTC 12630, LMG 23739)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003332855

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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