Sphingopyxis solisilvae (KEMB 9005-451, KACC 19003, JCM 31675)

Name: Sphingopyxis solisilvae (KEMB 9005-451, KACC 19003, JCM 31675)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140477

Type strain

Strain Designation R366

Culture col. no. KEMB 9005-451 KACC 19003 JCM 31675 R366

NCBI tax ID(s) 1886788

Special Collections JCM Literature strains

Links

Sphingopyxis solisilvae R366 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from forest soil sample.

Gram-negative motile rod-shaped colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 393625

JCM 31675

@ref 20215

Last LPSN update 2025-12-16 10:03:36

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingopyxis

Species Sphingopyxis solisilvae

Full scientific name Sphingopyxis solisilvae Chaudhary et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
43250	negative	1.2-1.4 µm	0.3-0.6 µm	rod-shaped	monotrichous, polar
125439	negative					95.9
125438	negative					94.494

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43250	0.5-0.8 mm	yellow	circular	5 days	R2A

Culture and growth conditions

Culture medium

@ref	Name	Growth
43250	Reasoner's 2A agar (R2A)
43250	nutritient agar (NA)
43250	trypticase soy agar (TSA)
43250	veal infusion agar
43250	brain heart infusion agar
43250	MacConkey agar
43250	marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43250	positive	optimum	25-35	mesophilic
43250	positive	growth	15-42
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
43250	positive	optimum	7.0-8.0
43250	positive	growth	6.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43250	aerobe
125439	obligate aerobe	98.4

Spore formation

@ref	Spore formation	Confidence
43250
125439		95.3
125438		93.539

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43250	NaCl	positive	growth	0-4 %
43250	NaCl	positive	optimum	0 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43250	37054 ChEBI	3-hydroxybutyrate	+	carbon source
43250	17128 ChEBI	adipate	-	assimilation
43250	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
43250		casein	+	hydrolysis
43250	17029 ChEBI	chitin	-	hydrolysis
43250	17634 ChEBI	D-glucose	-	assimilation
43250	16899 ChEBI	D-mannitol	-	assimilation
43250	16024 ChEBI	D-mannose	-	assimilation
43250	27689 ChEBI	decanoate	-	assimilation
43250	16991 ChEBI	dna	-	hydrolysis
43250	4853 ChEBI	esculin	-	hydrolysis
43250		esculin ferric citrate	-	hydrolysis
43250	5291 ChEBI	gelatin	-	hydrolysis
43250	17234 ChEBI	glucose	-	fermentation
43250	30849 ChEBI	L-arabinose	-	assimilation
43250	17203 ChEBI	L-proline	+	carbon source
43250	25115 ChEBI	malate	-	assimilation
43250	17306 ChEBI	maltose	-	assimilation
43250	506227 ChEBI	N-acetylglucosamine	-	assimilation
43250	17632 ChEBI	nitrate	-	reduction
43250	18401 ChEBI	phenylacetate	-	assimilation
43250	32032 ChEBI	potassium gluconate	-	assimilation
43250	17272 ChEBI	propionate	+	carbon source
43250	53258 ChEBI	sodium citrate	-	assimilation
43250	28017 ChEBI	starch	-	hydrolysis
43250	9300 ChEBI	suberic acid	+	carbon source
43250	53423 ChEBI	tween 40	-	hydrolysis
43250	53426 ChEBI	tween 80	-	hydrolysis
43250	18186 ChEBI	tyrosine	-	hydrolysis
43250	16199 ChEBI	urea	-	hydrolysis
43250	31011 ChEBI	valerate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite
43250	15688 ChEBI	acetoin
43250	16136 ChEBI	hydrogen sulfide
43250	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
43250	15688 ChEBI	acetoin	-
43250	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
43250	acid phosphatase	+	3.1.3.2
43250	alkaline phosphatase	+	3.1.3.1
43250	alpha-chymotrypsin	-	3.4.21.1
43250	alpha-fucosidase	-	3.2.1.51
43250	alpha-galactosidase	-	3.2.1.22
43250	alpha-glucosidase	-	3.2.1.20
43250	alpha-mannosidase	-	3.2.1.24
43250	beta-galactosidase	-	3.2.1.23
43250	beta-glucuronidase	-	3.2.1.31
43250	catalase	-	1.11.1.6
43250	cystine arylamidase	+	3.4.11.3
43250	cytochrome oxidase	+	1.9.3.1
43250	esterase (C 4)	+
43250	esterase Lipase (C 8)	+
43250	leucine arylamidase	+	3.4.11.1
43250	lipase (C 14)	-
43250	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43250	naphthol-AS-BI-phosphohydrolase	+
43250	trypsin	-	3.4.21.4
43250	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43250

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	32.8
C16:1ω7c / C16:1ω6c	19
C17:1ω6c	15
C16:0	12.4
C18:1ω7c 11-methyl	7.4
C14:0 2OH	2.6
C15:0 2OH	2.2
C16:0 2OH	2
C16:1ω5c	1.8
C17:0	1.5
C17:1ω8c	1.2
C18:1ω5c	0.7
C14:0	0.5
C18:0	0.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
43250	forest soil sample	Kyonggi University, Suwon	Republic of Korea	KOR	Asia	37	127 37/127	R2A medium (MB Cell)	2 weeks	28
67770	Forest soil of Kyonggi Univ.		Republic of Korea	KOR	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1547587v1 assembly for Sphingopyxis solisilvae R366	scaffold	GCA_015475875	1886788.3	2995902960	1886788	64.25

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43250	Sphingopyxis solisilvae strain R366 16S ribosomal RNA gene, partial sequence	KX672815	1409		1886788

GC content

@ref	GC-content (mol%)	Method
43250	65.1	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: Sphingopyxis solisilvae R366
NCBI: GCA_015475875

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.30	no
125439	motility	BacteriaNetⓘ	yes	58.30	no
125439	gram_stain	BacteriaNetⓘ	negative	95.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingopyxis solisilvae R366
NCBI: GCA_015475875.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.49	no
125438	anaerobic	anaerobicⓘ	no	95.29	yes
125438	aerobic	aerobicⓘ	yes	89.12	no
125438	spore-forming	spore-formingⓘ	no	93.54	no
125438	thermophilic	thermophileⓘ	no	95.20	yes
125438	flagellated	motile2+ⓘ	yes	65.69	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingopyxis solisilvae sp. nov., isolated from forest soil.	Chaudhary DK, Dahal RH, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001869	2017

References

#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 )
#43250	Dhiraj Kumar Chaudhary, Ram Hari Dahal, Jaisoo Kim: Sphingopyxis solisilvae sp. nov., isolated from forest soil. IJSEM 67: 1820 - 1826 2017 ( DOI 10.1099/ijsem.0.001869 , PubMed 28613148 )
#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;
#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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Sphingopyxis solisilvae (KEMB 9005-451, KACC 19003, JCM 31675)

Name and taxonomic classification