Sphingomonas parapaucimobilis (DSM 7463, ATCC 51231, GIFU 11387)

Name: Sphingomonas parapaucimobilis (DSM 7463, ATCC 51231, GIFU 11387)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14220

Type strain

Strain Designation OH 3807

Culture col. no. DSM 7463 ATCC 51231 GIFU 11387 IAM 14268 JCM 7510 9 more

NCBI tax ID(s) 1219049 28213

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- JCM <- GIFU <- H. Yamanaka JCM <-- GIFU 11387 <-- Y. Yamanaka OH 3807. CIP <- 2000, CCM <- GIFU <- H. Yamanaka: strain OH 3807

Links

Sphingomonas parapaucimobilis OH 3807 is an aerobe, Gram-negative, motile bacterium that was isolated from urine.

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

Name and taxonomic classification

SI-ID 4984

LMG 10923,ATCC 51231,CCUG 27291,DSM 7463,IFO 15100,JCM 7510,CIP 106724,CCM 4599,IAM 14268,KCTC 2815,NBRC 15100,HAMBI 1833,NCIMB 13745,BCRC 17635,CCRC 17635

@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 parapaucimobilis

Full scientific name Sphingomonas parapaucimobilis Yabuuchi et al. 1990

BacDive ID	Other strains from **Sphingomonas parapaucimobilis** (3)	Type strain
144957	S. parapaucimobilis CCUG 27292, JCM 7512, GIFU 2135, IFO 15101, ...
165544	S. parapaucimobilis JCM 7517, GIFU 2266
165547	S. parapaucimobilis JCM 7520, GIFU 11693

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		95.639
125439	negative		92.7
121573	negative	rod-shaped

Pigmentation

@ref	Production	Name
121573		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3168	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
35211	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121573	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3168	positive	growth	28
35211	positive	growth	30
48700	positive	growth	30
67770	positive	growth	30
121573	positive	growth	25-37
121573	negative	growth	5
121573	negative	growth	10
121573	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
48700	aerobe
121573	obligate aerobe
125439	obligate aerobe	98.389

Spore formation

@ref	Spore formation	Confidence
125439		98.512

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121573	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: Q-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
121573	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
121573	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
121573	17632 ChEBI	nitrate	+	reduction
121573	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121573	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121573	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121573	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
121573	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-mannosidase	-	3.2.1.24	from API zym
121573	amylase	-
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
121573	caseinase	-	3.4.21.50
121573	catalase	+	1.11.1.6
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
121573	DNase	-
121573	gelatinase	+/-
68369	gelatinase	-		from API 20NE
121573	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121573	lipase	-
121573	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
121573	ornithine decarboxylase	-	4.1.1.17
121573	oxidase	-
121573	protease	-
121573	tryptophan deaminase	-
121573	tween esterase	-
121573	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
48700	-	+	-	-	-	+	+	-	-	-	+	+	-	+	-	+	+	+	-	-
121573	-	+	+	+	+	+	+	+	+	-	+	+	-	+	+	-	+	+	-	-

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
48700	+	-	-	-	-	+	-	+	+	+	+	-	+	+	-	-	-	+	+	-	+

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
121573	not determinedn.d.	+	+	-	+	+	-	+	+	+	+	+	+	+	-	-	+	+	-	+	-	+	+	+	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Fluids	#Urine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
3168	urine	Japan	JPN	Asia
48700	Urine
67770	Urine
121573	Urine	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB680767 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	518
Soil Samples	167
Animal Samples	1394
Plant Samples	394
Total Samples	2473

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3168	2	Risk group (German classification) According to TRBA 466
121573	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	ASM78771v1 assembly for Sphingomonas parapaucimobilis NBRC 15100	contig	GCA_000787715	1219049.3	2630968314	1219049	53

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Sphingomonas parapaucimobilis 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	GQ907188	729	28213
20218	Sphingomonas parapaucimobilis 16S ribosomal RNA, partial sequence	D38424	156	28213
20218	Sphingomonas parapaucimobilis gene for 16S rRNA, partial sequence	D13724	1418	28213
20218	Sphingomonas parapaucimobilis gene for 16S rRNA	D84525	1388	28213
20218	Sphingomonas parapaucimobilis partial 16S rRNA gene	X72721	1408	28213
20218	Sphingomonas parapaucimobilis gene for 16S rRNA, partial sequence, strain: NBRC 15100	AB680767	1416	28213

GC content

@ref	GC-content (mol%)	Method
3168	64.7	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: ASM78771v1 assembly for Sphingomonas parapaucimobilis NBRC 15100
BV-BRC: 1219049.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.39	no
125439	gram_stain	BacteriaNetⓘ	negative	92.70	no
125439	motility	BacteriaNetⓘ	yes	47.93	no
125439	spore_formation	BacteriaNetⓘ	no	98.51	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas parapaucimobilis NBRC 15100
PATRIC: 1219049.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.64	no
125438	anaerobic	anaerobicⓘ	no	96.50	yes
125438	spore-forming	spore-formingⓘ	no	89.03	no
125438	aerobic	aerobicⓘ	yes	86.40	no
125438	thermophilic	thermophileⓘ	no	97.29	no
125438	flagellated	motile2+ⓘ	yes	66.86	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Evidence for natural horizontal transfer of the pcpB gene in the evolution of polychlorophenol-degrading sphingomonads.	Tiirola MA, Wang H, Paulin L, Kulomaa MS.	Appl Environ Microbiol	10.1128/aem.68.9.4495-4501.2002	2002
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	Aromatic-degrading Sphingomonas isolates from the deep subsurface.	Fredrickson JK, Balkwill DL, Drake GR, Romine MF, Ringelberg DB, White DC.	Appl Environ Microbiol	10.1128/aem.61.5.1917-1922.1995	1995
Metabolism	Isolation and characterization of Sphingomonadaceae from fouled membranes.	de Vries HJ, Beyer F, Jarzembowska M, Lipinska J, van den Brink P, Zwijnenburg A, Timmers PHA, Stams AJM, Plugge CM.	NPJ Biofilms Microbiomes	10.1038/s41522-018-0074-1	2019
	Alterations in intestinal microbiota and enzyme activities under cold-humid stress: implications for diarrhea in cold-dampness trapped spleen syndrome.	Wu Y, Deng N, Liu J, Jiang P, Tan Z.	Front Microbiol	10.3389/fmicb.2023.1288430	2023
Phylogeny	Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas.	Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T, Yamamoto H	Microbiol Immunol	10.1111/j.1348-0421.1990.tb00996.x	1990

References

#3168	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7463
#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 )
#35211	; Curators of the CIP;
#48700	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 27291
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#121573	Collection of Institut Pasteur ; Curators of the CIP; CIP 106724
#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 )

Content

About us

Sphingomonas parapaucimobilis (DSM 7463, ATCC 51231, GIFU 11387)

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

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_000787715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media