Name: Sphingomonas parapaucimobilis OH 3807
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14220

Type strain:

Species: Sphingomonas parapaucimobilis

Strain Designation: OH 3807

Culture col. no.: DSM 7463, ATCC 51231, GIFU 11387, IAM 14268, JCM 7510, NCIMB 13745, CCUG 27291, LMG 10923, BCRC 17635, CCM 4599, CIP 106724, IFO 15100, NBRC 15100

Strain history: CIP <- 2000, CCM <- GIFU <- H. Yamanaka: strain OH 3807

NCBI tax ID(s): 1219049 (strain), 28213 (species)

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

Special Collections

Other strains from Sphingomonas parapaucimobilis

Section

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

Gram-negative
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas parapaucimobilis**
	Full Scientific Name (LPSN)	Sphingomonas parapaucimobilis Yabuuchi et al. 1990

Information on morphological and physiological properties Morphology

[Ref.: #121573]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %95.639

[Ref.: #121573]	Cell shape	rod-shaped

[Ref.: #121573]	Motility	yes

[Ref.: #121573]	Pigment production	no
[Ref.: #121573]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3168]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #3168]

Culture medium growth

[Ref.: #3168]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3168]

Culture medium composition

expand / minimize

[Ref.: #35211]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #35211]

Culture medium growth

[Ref.: #35211]

Culture medium composition

expand / minimize

[Ref.: #121573]

Culture medium

CIP Medium 72

[Ref.: #121573]

Culture medium growth

[Ref.: #121573]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #3168]		growth	28 °C
[Ref.: #35211]		growth	30 °C
[Ref.: #48700]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #121573]		growth	25-37 °C
[Ref.: #121573]	no	growth	5 °C
[Ref.: #121573]	no	growth	10 °C
[Ref.: #121573]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #48700]	Oxygen tolerance	aerobe
[Ref.: #121573]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #121573]		NaCl		growth	0-10	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #121573]	citrate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #121573]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #121573]	nitrate ChEBI	+	reduction
[Ref.: #121573]	nitrate ChEBI	-	respiration
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #121573]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #121573]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #121573]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121573]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #121573]	amylase	-
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE, API zym
[Ref.: #121573]	caseinase	-	3.4.21.50
[Ref.: #121573]	catalase	+	1.11.1.6
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #121573]	DNase	-
[Ref.: #121573]	gelatinase	+/-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #121573]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121573]	lipase	-
[Ref.: #121573]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121573]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121573]	oxidase	-
[Ref.: #121573]	protease	-
[Ref.: #121573]	tryptophan deaminase	-
[Ref.: #121573]	tween esterase	-
[Ref.: #121573]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #48700]	7484	+	-	-	-	-	+	-	+	+	+	+	-	+	+	-	-	-	+	+	-	+

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	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
[Ref.: #121573]	1798	not determinedn.d.	+	+	-	+	+	-	+	+	+	+	+	+	+	-	-	+	+	-	+	-	+	+	+	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #48700]	3807	-	+	-	-	-	+	+	-	-	-	+	+	-	+	-	+	+	+	-	-
[Ref.: #121573]	9755	-	+	+	+	+	+	+	+	+	-	+	+	-	+	+	-	+	+	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #3168]	Sample type/isolated from	urine
[Ref.: #3168]	Country	Japan
[Ref.: #3168]	Country ISO 3 Code	JPN
[Ref.: #3168]	Continent	Asia

[Ref.: #48700]	Sample type/isolated from	Urine

[Ref.: #67770]	Sample type/isolated from	Urine

[Ref.: #121573]	Sample type/isolated from	Urine
[Ref.: #121573]	Country	Japan
[Ref.: #121573]	Country ISO 3 Code	JPN
[Ref.: #121573]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host Body Product

#Fluids

#Urine

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #3168]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #121573]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #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	GenBank ENA	28213 tax ID	*
[Ref.: #20218]	Sphingomonas parapaucimobilis 16S ribosomal RNA, partial sequence	D38424	156	GenBank ENA	28213 tax ID	*
[Ref.: #20218]	Sphingomonas parapaucimobilis gene for 16S rRNA, partial sequence	D13724	1418	GenBank ENA	28213 tax ID	*
[Ref.: #20218]	Sphingomonas parapaucimobilis gene for 16S rRNA	D84525	1388	GenBank ENA	28213 tax ID	*
[Ref.: #20218]	Sphingomonas parapaucimobilis partial 16S rRNA gene	X72721	1408	GenBank ENA	28213 tax ID	*
[Ref.: #20218]	Sphingomonas parapaucimobilis gene for 16S rRNA, partial sequence, strain: NBRC 15100	AB680767	1416	GenBank ENA	28213 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Sphingomonas parapaucimobilis NBRC 15100	GCA_000787715	contig	GenBank ENA	1219049 tax ID
[Ref.: #66792]	Sphingomonas parapaucimobilis NBRC 15100	1219049.3	wgs	PATRIC	1219049 tax ID	*
[Ref.: #66792]	Sphingomonas parapaucimobilis NBRC 15100	2630968314	draft	JGI IMG/M	1219049 tax ID	*

[Ref.: #3168]

GC-content

64.7 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sphingomonas parapaucimobilis NBRC 15100 PATRIC: 1219049.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomonas parapaucimobilis NBRC 15100 PATRIC: 1219049.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.639	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.502	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.029	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.395	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.288	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	66.858	no

Availability in culture collections External links

[Ref.: #3168]

Culture collection no.

DSM 7463, ATCC 51231, GIFU 11387, IAM 14268, JCM 7510, NCIMB 13745, CCUG 27291, LMG 10923, BCRC 17635, CCM 4599, CIP 106724, IFO 15100, NBRC 15100

[Ref.: #83379]

SI-ID 4984

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#83379

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID4984.1 )

#121573 Collection of Institut Pasteur ; Curators of the CIP; CIP 106724
* These data were automatically processed and therefore are not curated

Change proposal

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Search for species Sphingomonas parapaucimobilis in external resources:
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Sphingomonas parapaucimobilis NBRC 15100

Sphingomonas parapaucimobilis NBRC 15100

Change proposal

Change proposal