Sphingopyxis granuli (DSM 17810, KCTC 12209, NBRC 100800)

Name: Sphingopyxis granuli (DSM 17810, KCTC 12209, NBRC 100800)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14281

Type strain

Strain Designation Kw07

Culture col. no. DSM 17810 KCTC 12209 NBRC 100800 CCUG 52902 Kw07

NCBI tax ID(s) 1219060 267128

Special Collections DSMZ CCUG KCTC

History <- S.-T. Lee, KAIST <- W.-T. Im, KAIST; Kw07 <- ST Lee, KAIST

Links

Sphingopyxis granuli Kw07 is an aerobe, Gram-negative bacterium that was isolated from granules from a wastewater treatment plant of a brewery.

Gram-negative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 132667

KCTC 12209,CCUG 52902,NBRC 100800,DSM 17810

@ref 20215

Last LPSN update 2026-02-09 11:21:22

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingopyxis

Species Sphingopyxis granuli

Full scientific name Sphingopyxis granuli Kim et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	negative
125438	negative	95.333
125439	negative	99

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7201	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7201	positive	growth	28
59720	positive	growth	30-37
67771	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
59720	aerobe
67771	aerobe
125439	obligate aerobe	98.9

Spore formation

@ref	Spore formation	Confidence
125439		97.9

Observation

67771

Observationquinones: Q-10

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	cardiolipin biosynthesis	100	7 of 7
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	cyanate degradation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	NAD metabolism	83.33	15 of 18
66794	tryptophan metabolism	81.58	31 of 38
66794	methionine metabolism	80.77	21 of 26
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	vitamin B1 metabolism	76.92	10 of 13
66794	toluene degradation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	histidine metabolism	72.41	21 of 29
66794	glutathione metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	phenol degradation	70	14 of 20
66794	degradation of sugar alcohols	68.75	11 of 16
66794	lipid metabolism	67.74	21 of 31
66794	cysteine metabolism	66.67	12 of 18
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	d-mannose degradation	66.67	6 of 9
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	lysine metabolism	66.67	28 of 42
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	tyrosine metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	arginine metabolism	62.5	15 of 24
66794	sulfate reduction	61.54	8 of 13
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	non-pathway related	60.53	23 of 38
66794	gallate degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	oxidative phosphorylation	57.14	52 of 91
66794	propanol degradation	57.14	4 of 7
66794	lipid A biosynthesis	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	resorcinol degradation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	vitamin B12 metabolism	50	17 of 34
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	glycogen biosynthesis	50	2 of 4
66794	carnitine metabolism	50	4 of 8
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	d-xylose degradation	45.45	5 of 11
66794	cholesterol biosynthesis	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	degradation of hexoses	44.44	8 of 18
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	metabolism of disaccharids	36.36	4 of 11
66794	chlorophyll metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	catecholamine biosynthesis	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Water treatment plant

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7201	granules from a wastewater treatment plant of a brewery	Kwang-Ju	Republic of Korea	KOR	Asia
67771	From granule sludge		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB681243 (>99% sequence identity) for Sphingopyxis granuli from Microbeatlas

Aquatic Samples	35
Soil Samples	38
Animal Samples	11
Plant Samples	8
Total Samples	92

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7201	1	Risk group (German 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	ASM159104v1 assembly for Sphingopyxis granuli NBRC 100800	contig	GCA_001591045	1219060.3	2731957635	1219060	37.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Sphingopyxis granuli gene for 16S rRNA, partial sequence, strain: NBRC 100800	AB681243	1414		1219060
7201	Sphingopyxis granuli strain Kw07 16S ribosomal RNA gene, partial sequence	AY563034	1422		1219060

GC content

7201

GC-content (mol%)63.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingopyxis granuli NBRC 100800
NCBI: GCA_001591045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.00	no
125439	motility	BacteriaNetⓘ	yes	61.10	no
125439	spore_formation	BacteriaNetⓘ	no	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingopyxis granuli NBRC 100800
PATRIC: 1219060.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.33	yes
125438	anaerobic	anaerobicⓘ	no	95.34	yes
125438	spore-forming	spore-formingⓘ	no	89.80	no
125438	aerobic	aerobicⓘ	yes	87.58	yes
125438	thermophilic	thermophileⓘ	no	95.58	yes
125438	flagellated	motile2+ⓘ	yes	60.77	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Genome-Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of Sphingopyxis.	Yang F, Feng H, Massey IY, Huang F, Guo J, Zhang X.	Biomed Res Int	10.1155/2020/5849123	2020
Phylogeny	Sphingopyxis lindanitolerans sp. nov. strain WS5A3p(T) enriched from a pesticide disposal site.	Kaminski MA, Sobczak A, Spolnik G, Danikiewicz W, Dziembowski A, Lipinski L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003094	2018
Phylogeny	Sphingopyxis italica sp. nov., isolated from Roman catacombs.	Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijs.0.046573-0	2012
Phylogeny	Sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in alpha-4 subclass of the Proteobacteria.	Kim MK, Im WT, Ohta H, Lee M, Lee ST	J Microbiol	2169	2005

References

#7201	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17810
#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 )
#59720	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52902
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 granuli (DSM 17810, KCTC 12209, NBRC 100800)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001591045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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