Sphingomonas mali (DSM 10565, IFO 15500, NBRC 15500)

Name: Sphingomonas mali (DSM 10565, IFO 15500, NBRC 15500)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14224

Type strain

Strain Designation Y-347

Culture col. no. DSM 10565 IFO 15500 NBRC 15500 Y-347 LMG 17331 6 more

NCBI tax ID(s) 1219048 40682

Special Collections DSMZ JCM KCTC CIP

History DSMZ <- IFO <- M. Takeuchi; Y-347 JCM <-- IFO 15500 <-- M. Yasuda Y-347. CIP <- 2002, JCM <- IFO <- M. Yasuda: strain Y-347

Links

Sphingomonas mali Y-347 is a Gram-negative, motile, rod-shaped bacterium that was isolated from roots of apple tree.

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

Name and taxonomic classification

SI-ID 14406

LMG 17331,ATCC 51840,DSM 10565,IFO 15500,JCM 10193,KCTC 2826,NCIMB 13412,CIP 107356,NBRC 15500,HAMBI 2070,IAM 14460,BCRC 17403,CCRC 17403

@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 mali

Full scientific name Sphingomonas mali Takeuchi et al. 1995

Synonyms (1)

Alterisphingomonas mali

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125439	negative		94.06
125438	negative		96.501
120758	negative	rod-shaped

Pigmentation

@ref	Production	Name
120758		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3977	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33115	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120758	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3977	positive	growth	30
33115	positive	growth	30
67770	positive	growth	30
120758	positive	growth	25-30
120758	negative	growth	5
120758	negative	growth	10
120758	negative	growth	37
120758	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.202

Spore formation

@ref	Spore formation	Confidence
125439		97.567

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120758	NaCl	positive	growth	0 %
120758	NaCl		growth	2 %
120758	NaCl		growth	4 %
120758	NaCl		growth	6 %
120758	NaCl		growth	8 %
120758	NaCl		growth	10 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120758	16947 ChEBI	citrate	-	carbon source
120758	4853 ChEBI	esculin	+	hydrolysis
120758	17632 ChEBI	nitrate	-	reduction
120758	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
120758	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120758	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120758	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
68382	beta-galactosidase	-	3.2.1.23	from API zym
120758	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120758	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120758	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120758	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
120758	ornithine decarboxylase	-	4.1.1.17
120758	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
120758	tryptophan deaminase	-
120758	urease	-	3.5.1.5
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
120758	-	+	+	+	-	+	+	+	-	-	+	+	-	-	-	+	-	-	-	-

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
120758	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	Country	Country ISO 3 Code	Continent
3977	roots of apple tree	Japan	JPN	Asia
67770	Apple tree roots
120758		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence Y09638 (>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
3977	1	Risk group (German classification) According to TRBA 466
120758	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	ASM159841v1 assembly for Sphingomonas mali NBRC 15500	contig	GCA_001598415	1219048.3	2681812977	1219048	54.47

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Sphingomonas mali gene for 16S rRNA, partial sequence, strain: NBRC 15500	AB680884	1412	40682
20218	Sphingomonas mali gene for 16S rRNA, partial sequence, strain:IFO15500	D28576	829	40682
20218	S.mali 16S rRNA gene	Y09638	1442	40682
124043	Sphingomonas mali NBRC 15500 gene for 16S rRNA, partial sequence.	LC752390	562	40682
124043	Sphingomonas mali 16S ribosomal RNA gene, partial sequence 16S-23S ribosomal RNA intergenic spacer, complete sequence and 23S ribosomal RNA gene, partial sequence.	GQ907181	656	40682

GC content

@ref	GC-content (mol%)	Method
3977	65.9
67770	65.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM159841v1 assembly for Sphingomonas mali NBRC 15500
BV-BRC: 1219048.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	94.06	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no
125439	motility	BacteriaNetⓘ	yes	44.13	no
125439	spore_formation	BacteriaNetⓘ	no	97.57	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas mali NBRC 15500
PATRIC: 1219048.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.50	no
125438	anaerobic	anaerobicⓘ	no	96.03	no
125438	spore-forming	spore-formingⓘ	no	84.99	no
125438	aerobic	aerobicⓘ	yes	87.65	no
125438	thermophilic	thermophileⓘ	no	99.39	yes
125438	flagellated	motile2+ⓘ	yes	70.51	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	In vitro study of the ecotoxicological risk of methylisothiazolinone and chloroxylenol towards soil bacteria.	Nowak-Lange M, Niedzialkowska K, Bernat P, Lisowska K.	Sci Rep	10.1038/s41598-022-22981-9	2022
	Markerless gene deletion system for sphingomonads.	Kaczmarczyk A, Vorholt JA, Francez-Charlot A.	Appl Environ Microbiol	10.1128/aem.07347-11	2012
	An Isolated Arthrobacter sp. Enhances Rice (Oryza sativa L.) Plant Growth.	Chhetri G, Kim I, Kang M, So Y, Kim J, Seo T.	Microorganisms	10.3390/microorganisms10061187	2022
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
Phylogeny	Sphingomonas crusticola sp. nov., isolated from biological soil crusts.	Zhang K, Tang K, Feng F, Yuan B, Zhang X, Meng J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002074	2017
Phylogeny	Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng.	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

#3977	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10565
#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 )
#33115	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#120758	Collection of Institut Pasteur ; Curators of the CIP; CIP 107356
#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 mali (DSM 10565, IFO 15500, NBRC 15500)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001598415

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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