Sphingomonas pruni (DSM 10566, IFO 15498, NBRC 15498)

Name: Sphingomonas pruni (DSM 10566, IFO 15498, NBRC 15498)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14225

Type strain

Strain Designation Y-250, EY4228

Culture col. no. DSM 10566 IFO 15498 NBRC 15498 Y-250 CIP 107352 5 more

NCBI tax ID(s) 1219052 40683

Special Collections DSMZ JCM KCTC CIP

History DSMZ <- IFO <- M. Takeuchi; Y-250 CIP <- 2002, JCM <- 1998, E. Yabuuchi: strain EY4228 <- IFO <- M. Yasuda, Minist. Agric. Forest. Fish: strain Y-250

Links

Sphingomonas pruni Y-250 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from roots of Prunus persica.

Gram-negative motile rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92559

LMG 17327,DSM 10566,IFO 15498,LMG 17538,LMG 18380,ATCC 51838,JCM 10277,NCIMB 13411,KCTC 2824,CIP 107352,NBRC 15498,HAMBI 2069,IAM 14461,BCRC 17402,CCRC 17402

@ref 20215

Last LPSN update 2026-05-29 08:28:14

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas pruni

Full scientific name Sphingomonas pruni Takeuchi et al. 1995

Synonyms (1)

Alterisphingomonas pruni

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		97.494
125439	negative		95.318
121977	negative	rod-shaped

Pigmentation

@ref	Production	Name
121977		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3978	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
32679	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121977	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3978	positive	growth	30
32679	positive	growth	30
121977	positive	growth	10-37
121977	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121977	obligate aerobe
125439	obligate aerobe	99.68

Spore formation

@ref	Spore formation	Confidence
125439		98.503

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121977	NaCl	positive	growth	0 %
121977	NaCl		growth	2 %
121977	NaCl		growth	4 %
121977	NaCl		growth	6 %
121977	NaCl		growth	8 %
121977	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
121977	16947 ChEBI	citrate	-	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
121977	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
121977	17632 ChEBI	nitrate	+	reduction
121977	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121977	16301 ChEBI	nitrite	+	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121977	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
121977	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
121977	beta-galactosidase	+	3.2.1.23
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
121977	caseinase	-	3.4.21.50
121977	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
121977	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121977	gelatinase	+/-
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121977	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
121977	ornithine decarboxylase	-	4.1.1.17
121977	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
121977	tryptophan deaminase	-
121977	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
121977	-	+	+	+	-	+	+	+	+	-	+	+	-	+	+	+	+	-	-	-

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
3978	-	-	-	-	-	+	-	+	+	+	+	-	+	+	+	-	-	+	-	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121977	not determinedn.d.	+	-	+	+	+	-	-	-	-	+	+	+	-	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent	Isolation date
3978	roots of Prunus persica	Prunus persica	Japan	JPN	Asia
121977			Japan	JPN	Asia	1992

Taxonmaps

69479

Global distribution of 16S sequence Y09637 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	484
Soil Samples	1345
Animal Samples	298
Plant Samples	258
Total Samples	2385

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3978	1	Risk group (German classification) According to TRBA 466
121977	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
66792	ASM159845v1 assembly for Sphingomonas pruni NBRC 15498	contig	GCA_001598455	1219052.3	2731957701	1219052	44.76

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Sphingomonas pruni gene for 16S rRNA, partial sequence, strain: NBRC 15498	AB680882	1412	40683
20218	Sphingomonas pruni gene for 16S rRNA, partial sequence, strain:IFO15498	D28570	829	40683
3978	S.pruni 16S rRNA gene	Y09637	1442	40683
124043	Sphingomonas pruni 16S ribosomal RNA gene, partial sequence 16S-23S ribosomal RNA intergenic spacer, complete sequence and 23S ribosomal RNA gene, partial sequence.	GQ907180	544	40683

GC content

3978

GC-content (mol%)65.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM159845v1 assembly for Sphingomonas pruni NBRC 15498
BV-BRC: 1219052.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	95.32	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.68	no
125439	motility	BacteriaNetⓘ	yes	48.05	no
125439	spore_formation	BacteriaNetⓘ	no	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas pruni NBRC 15498
PATRIC: 1219052.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.49	no
125438	anaerobic	anaerobicⓘ	no	95.97	yes
125438	spore-forming	spore-formingⓘ	no	88.03	no
125438	aerobic	aerobicⓘ	yes	87.71	yes
125438	thermophilic	thermophileⓘ	no	98.39	yes
125438	flagellated	motile2+ⓘ	yes	68.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil.	Nogales B, Moore ER, Llobet-Brossa E, Rossello-Mora R, Amann R, Timmis KN.	Appl Environ Microbiol	10.1128/aem.67.4.1874-1884.2001	2001
Metabolism	Comprehensive Genome Analysis on the Novel Species Sphingomonas panacis DCY99^T Reveals Insights into Iron Tolerance of Ginseng.	Kim YJ, Park JY, Balusamy SR, Huo Y, Nong LK, Thi Le H, Yang DC, Kim D.	Int J Mol Sci	10.3390/ijms21062019	2020
Phylogeny	16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads.	Tokajian S, Issa N, Salloum T, Ibrahim J, Farah M.	Front Microbiol	10.3389/fmicb.2016.00149	2016
Metabolism	The growth of Steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to Rhizobiales.	Sakai M, Hosoda A, Ogura K, Ikenaga M.	Microbes Environ	10.1264/jsme2.me13169	2014
Phylogeny	Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng.	Singh P, Singh P, Kim YJ, Hoang VA, Farh Mel-A, Yang DC.	Antonie Van Leeuwenhoek	10.1007/s10482-015-0527-y	2015
Phylogeny	Sphingomonas yantingensis sp. nov., a mineral-weathering bacterium isolated from purplish paddy soil.	Huang J, Huang Z, Zhang ZD, He LY, Sheng XF	Int J Syst Evol Microbiol	10.1099/ijs.0.055954-0	2013
Phylogeny	Sphingomonas kaistensis sp. nov., a novel alphaproteobacterium containing pufLM genes.	Kim MK, Schubert K, Im WT, Kim KH, Lee ST, Overmann J	Int J Syst Evol Microbiol	10.1099/ijs.0.64579-0	2007
Phylogeny	Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan.	Asker D, Beppu T, Ueda K	Int J Syst Evol Microbiol	10.1099/ijs.0.64828-0	2007
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
Phylogeny	Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations.	Ohta H, Hattori R, Ushiba Y, Mitsui H, Ito M, Watanabe H, Tonosaki A, Hattori T	Int J Syst Evol Microbiol	10.1099/ijs.0.02959-0	2004
Phylogeny	Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.	Takeuchi M, Sakane T, Yanagi M, Yamasato K, Hamana K, Yokota A	Int J Syst Bacteriol	10.1099/00207713-45-2-334	1995

References

#3978	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10566
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#32679	; 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) .
#68369	Automatically annotated from API 20NE .
#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 .
#121977	Collection of Institut Pasteur ; Curators of the CIP; CIP 107352
#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 pruni (DSM 10566, IFO 15498, NBRC 15498)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001598455

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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