Sphingomonas soli (DSM 18313, IAM 15213, KCTC 12210)

Name: Sphingomonas soli (DSM 18313, IAM 15213, KCTC 12210)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14245

Type strain

Strain Designation T5-04, T5-04,52.101

Culture col. no. DSM 18313 IAM 15213 KCTC 12210 NBRC 10081 T5-04 4 more

NCBI tax ID(s) 1219055 266127

Special Collections DSMZ JCM KCTC Literature strains CIP

Links

Sphingomonas soli T5-04 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 122342

KCTC 12210,IAM 15213,NBRC 100801,DSM 18313,JCM 21668,CIP 109210

@ref 20215

Last LPSN update 2025-12-16 09:50:18

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas soli

Full scientific name Sphingomonas soli Yang et al. 2006

Synonyms (1)

Alteristakelama soli

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31577	negative	1 µm	1 µm	rod-shaped
67771	negative
122664	negative			rod-shaped
125438	negative				96.758
125439	negative				94.5

Pigmentation

31577

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7497	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
37476	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122664	CIP Medium 566	Medium recipe at CIP
122664	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7497	positive	growth	30	mesophilic
31577	positive	growth	15-37
31577	positive	optimum	30	mesophilic
37476	positive	growth	25	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31577	positive	optimum	6.8-7.5
31577	positive	growth	6.8-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31577	aerobe
67771	aerobe
122664	microaerophile
125439	aerobe	97.9

Spore formation

@ref	Spore formation	Confidence
31577
125439		92.9

Observation

@ref	Observation
31577	aggregates in chains
67771	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31577	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
31577	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
122664	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
122664	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
31577	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
122664	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122664	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31577	catalase	+	1.11.1.6
122664	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31577	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
122664	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122664	ornithine decarboxylase	-	4.1.1.17
122664	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
122664	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122664	-	+	+	+	-	+	+	-	+	-	+	+	-	-	-	-	+	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
7497	-	-	-	-	-	+	-	-	+	+	+	-	-	-	-	-	-	-	-	-	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122664	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
7497	soil of ginseng field	Daejeon	Republic of Korea	KOR	Asia
67770	Soil
67771	From compost		Republic of Korea	KOR	Asia
122664	Environment, Soil of a ginseng field	Daejeon	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB166883 (>99% sequence identity) for Sphingomonas soli subclade from Microbeatlas

Aquatic Samples	23
Soil Samples	41
Animal Samples	22
Plant Samples	13
Total Samples	99

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7497	1	Risk group (German classification) According to TRBA 466
122664	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM159102v1 assembly for Sphingomonas soli NBRC 100801	contig	GCA_001591025	1219055.3	2731957634	1219055	72.13

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7497	Sphingomonas soli gene for 16S rRNA, partial sequence	AB166883	1422		266127
124043	Sphingomonas soli gene for 16S rRNA, partial sequence, strain: NBRC 100801.	AB681244	1412		266127

GC content

@ref	GC-content (mol%)	Method
7497	63.9	high performance liquid chromatography (HPLC)
31577	63.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas soli NBRC 100801
NCBI: GCA_001591025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	97.90	no
125439	gram_stain	BacteriaNetⓘ	negative	94.50	no
125439	motility	BacteriaNetⓘ	yes	50.60	no
125439	spore_formation	BacteriaNetⓘ	no	92.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas soli NBRC 100801
PATRIC: 1219055.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.76	yes
125438	anaerobic	anaerobicⓘ	no	93.80	yes
125438	spore-forming	spore-formingⓘ	no	89.39	yes
125438	aerobic	aerobicⓘ	yes	83.29	no
125438	thermophilic	thermophileⓘ	no	96.98	no
125438	flagellated	motile2+ⓘ	yes	68.58	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae.	Marmo P, Thaller MC, Di Lallo G, Henrici De Angelis L, Poerio N, De Santis F, Fraziano M, Migliore L, D'Andrea MM.	Viruses	10.3390/v12080894	2020
Phylogeny	Genomic-based taxonomic classification of the order Sphingomonadales.	Wang Y, You H, Kong YH, Sun C, Wu LH, Kim SG, Lee JS, Xu L, Xu XW.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006769	2025
Phylogeny	Impact of Fertilisation on the Bacterial Core Microbiome of Grassland Soils: Abundance in the Field and Growth In Vitro.	Chamedjeu RR, Jani K, Jetter K, Wilhelm K, Schafer P, Wilfert L, Sommer S, Riedel CU.	Environ Microbiol Rep	10.1111/1758-2229.70235	2025
	UV-C Exposure Enhanced the Cd²⁺ Adsorption Capability of the Radiation-Resistant Strain Sphingomonas sp. M1-B02.	Li Y, Niu H, Li S, Yue M, Zhang G.	Microorganisms	10.3390/microorganisms12122620	2024
Phylogeny	Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively.	Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY, Ahn TY, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.055269-0	2013
Phylogeny	Sphingomonas soli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in the alpha-4 subgroup of the Proteobacteria.	Yang DC, Im WT, Kim MK, Ohta H, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63839-0	2006

References

#7497	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18313
#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 )
#27866	IJSEM 703 2006 ( DOI 10.1099/ijs.0.63839-0 , PubMed 16585680 )
#31577	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 #27866
#37476	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#122664	Collection of Institut Pasteur ; Curators of the CIP; CIP 109210
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 soli (DSM 18313, IAM 15213, KCTC 12210)

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

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001591025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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