Sphingomonas oligophenolica (DSM 17107, CIP 107926, JCM 12082)

Name: Sphingomonas oligophenolica (DSM 17107, CIP 107926, JCM 12082)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14240

Type strain

Strain Designation S213

Culture col. no. DSM 17107 CIP 107926 JCM 12082 S213 CCUG 56448

NCBI tax ID(s) 301154

Special Collections DSMZ JCM CIP Literature strains CCUG

History <- H. Ohta; S213 H. Ohta S213 <-- T. Hattori. CIP <- 2003, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain S213 <- T. Hattori

Links

Sphingomonas oligophenolica S213 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from paddy field soil.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 134451

CIP 107926,JCM 12082,DSM 17107,CCUG 56448

@ref 20215

Last LPSN update 2025-12-16 09:50:18

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas oligophenolica

Full scientific name Sphingomonas oligophenolica Ohta et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30117	negative	1.25 µm	0.5 µm	rod-shaped
121416	negative			rod-shaped

Pigmentation

30117

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6761	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
37290	MEDIUM 479 - for Sphingomonas oligophenolica		Distilled water make up to (1000.000 ml);Sodium chloride (0.250 g);Peptone (0.500 g);Beef extract (0.500 g)
121416	CIP Medium 479	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6761	positive	growth	28	mesophilic
30117	positive	growth	04-37
30117	positive	optimum	20.5	psychrophilic
37290	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
121416	negative	growth	37
121416	negative	growth	10
121416	negative	growth	5
121416	positive	growth	25-30	mesophilic
121416	negative	growth	41

Physiology and metabolism

Oxygen tolerance

30117

Oxygen toleranceaerobe

Spore formation

30117

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30117	NaCl	positive	growth	0-0.5 %
121416	NaCl	positive	growth	0 %
121416	NaCl		growth	2 %
121416	NaCl		growth	4 %
121416	NaCl		growth	6 %
121416	NaCl		growth	8 %
121416	NaCl		growth	10 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30117	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
30117	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
30117	17057 ChEBI	cellobiose	+	carbon source
121416	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
121416	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
30117	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
30117	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
30117	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
30117	24996 ChEBI	lactate	+	carbon source
30117	17716 ChEBI	lactose	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
30117	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
30117	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
30117	17632 ChEBI	nitrate	+	reduction
121416	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121416	16301 ChEBI	nitrite	-	reduction
30117	15361 ChEBI	pyruvate	+	carbon source
30117	16634 ChEBI	raffinose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
30117	18222 ChEBI	xylose	+	carbon source

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121416	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121416	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
121416	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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	+	3.2.1.23	from API zym
121416	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
30117	catalase	+	1.11.1.6
121416	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
30117	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121416	gelatinase	-
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121416	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
121416	ornithine decarboxylase	-	4.1.1.17
121416	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
121416	tryptophan deaminase	-
121416	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	ethanol fermentation	100	2 of 2
66794	denitrification	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	alanine metabolism	72.41	21 of 29
66794	purine metabolism	72.34	68 of 94
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	starch degradation	70	7 of 10
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	tyrosine metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	tryptophan metabolism	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	glycogen metabolism	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	pyrimidine metabolism	57.78	26 of 45
66794	propanol degradation	57.14	4 of 7
66794	d-mannose degradation	55.56	5 of 9
66794	lipid A biosynthesis	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	arginine metabolism	54.17	13 of 24
66794	lysine metabolism	52.38	22 of 42
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	acetate fermentation	50	2 of 4
66794	degradation of sugar alcohols	50	8 of 16
66794	biotin biosynthesis	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	toluene degradation	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	CMP-KDO biosynthesis	50	2 of 4
66794	nitrate assimilation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	urea cycle	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	oxidative phosphorylation	35.16	32 of 91
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	degradation of hexoses	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	degradation of pentoses	32.14	9 of 28
66794	carotenoid biosynthesis	31.82	7 of 22
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenol degradation	30	6 of 20
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	ascorbate metabolism	22.73	5 of 22

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
121416	-	+	+	+	-	+	-	+	-	-	+	+	-	+	-	+	-	+	-	-

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
6761	+	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	+	-	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-
#Condition	#Humid	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6761	paddy field soil	near Sendai	Japan	JPN	Asia
67770	Paddy soil
121416	Environment, Paddy field soil	Kasimadai	Japan	JPN	Asia	1976

Taxonmaps

69479

Global distribution of 16S sequence AB018439 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	55
Soil Samples	67
Animal Samples	47
Plant Samples	87
Total Samples	256

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6761	1	Risk group (German classification) According to TRBA 466
121416	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952291v1 assembly for Sphingomonas oligophenolica JCM 12082	scaffold	GCA_039522915	301154	57.91

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6761	Sphingomonas oligophenolica gene for 16S rRNA, partial sequence	AB018439	1306		301154

GC content

30117

GC-content (mol%)64.2

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas paeninsulae sp. nov., isolated from soil sampled at Fildes Peninsula, Antarctica.	Geng Y, Zhang Y, Qin K, Liu J, Tian J, Huang Y, Wei Z, Zhang F, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.003504	2019
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 aquatica sp. nov., isolated from tap water.	Choi GM, Jo JH, Kang MS, Kim MS, Lee SY, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.001682	2017
Phylogeny	Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China.	Piao AL, Feng XM, Nogi Y, Han L, Li Y, Lv J	Curr Microbiol	10.1007/s00284-015-0957-9	2015
Phylogeny	Sphingomonas hylomeconis sp. nov., isolated from the stem of Hylomecon japonica.	Akbar A, Chen C, Zhu L, Xin K, Cheng J, Yang Q, Zhao L, Zhang L, Shen X	Int J Syst Evol Microbiol	10.1099/ijsem.0.000532	2015
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	Prosthecate sphingomonads: proposal of Sphingomonas canadensis sp. nov.	Abraham WR, Estrela AB, Rohde M, Smit J, Vancanneyt M	Int J Syst Evol Microbiol	10.1099/ijs.0.048678-0	2013
Phylogeny	Sphingomonas glacialis sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite.	Zhang DC, Busse HJ, Liu HC, Zhou YG, Schinner F, Margesin R	Int J Syst Evol Microbiol	10.1099/ijs.0.023135-0	2010
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 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

References

#6761	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17107
#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 )
#26472	IJSEM 2185 2004 ( DOI 10.1099/ijs.0.02959-0 , PubMed 15545456 )
#30117	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26472
#37290	; Curators of the CIP;
#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 )
#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 .
#121416	Collection of Institut Pasteur ; Curators of the CIP; CIP 107926
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 oligophenolica (DSM 17107, CIP 107926, JCM 12082)

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

Pathway annotation

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039522915

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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