Stenotrophomonas koreensis (DSM 17805, JCM 13256, KCTC 12211)

Name: Stenotrophomonas koreensis (DSM 17805, JCM 13256, KCTC 12211)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17561

Type strain

Strain Designation TR6-01

Culture col. no. DSM 17805 JCM 13256 KCTC 12211 CCUG 53887 CIP 109170 1 more

NCBI tax ID(s) 266128

Special Collections DSMZ CCUG JCM KCTC CIP Literature strains

History DSMZ <- S.-T. Lee; TR6-01 <- W.-T. Im JCM <-- W.-T. Im TR6-01. KCTC <- ST Lee, KAIST CIP <- 2006, JCM <- 2005, W.T. Im, Korea Adv. Inst. Sci. and Technol., Daejon, Korea: strain TR6-01

Links

Stenotrophomonas koreensis TR6-01 is an aerobe, Gram-negative bacterium that was isolated from compost.

Gram-negative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 232745

KCTC 12211,LMG 23369,JCM 13256,DSM 17805,CIP 109170,CCUG 53887

@ref 20215

Last LPSN update 2026-05-29 08:29:02

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Stenotrophomonas

Species Stenotrophomonas koreensis

Full scientific name Stenotrophomonas koreensis Yang et al. 2006

Synonyms (1)

"Pedostenotrophomonas koreensis"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
67771	negative
125439	negative		97.956
125438	negative		98.5
120490	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7196	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
37460	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120490	CIP Medium 566	Medium recipe at CIP
120490	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7196	positive	growth	28
37460	positive	growth	37
60056	positive	growth	30-37
67770	positive	growth	30
67771	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
60056	aerobe
67771	aerobe
120490	obligate aerobe
125439	obligate aerobe	95.462

Spore formation

@ref	Spore formation	Confidence
125439		99.857

Observation

67771

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
22950	16808 ChEBI	2-dehydro-D-gluconate	-	growth
22950	16193 ChEBI	3-hydroxybenzoate	-	growth
22950	37054 ChEBI	3-hydroxybutyrate	-	growth
22950	17879 ChEBI	4-hydroxybenzoate	-	growth
22950	58143 ChEBI	5-dehydro-D-gluconate	-	growth
22950	30089 ChEBI	acetate	+	growth
22950	17128 ChEBI	adipate	-	growth
22950	16947 ChEBI	citrate	+	growth
22950	17634 ChEBI	D-glucose	+	growth
22950	16988 ChEBI	D-ribose	-	growth
22950	17924 ChEBI	D-sorbitol	-	growth
22950	27689 ChEBI	decanoate	-	growth
22950	4853 ChEBI	esculin	+	hydrolysis
22950	5291 ChEBI	gelatin	+	hydrolysis
22950	17234 ChEBI	glucose	-	builds acid from
22950	28087 ChEBI	glycogen	-	growth
22950	27570 ChEBI	histidine	+	growth
22950	17240 ChEBI	itaconate	-	growth
22950	16977 ChEBI	L-alanine	+	growth
22950	30849 ChEBI	L-arabinose	-	growth
22950	18287 ChEBI	L-fucose	-	growth
22950	17203 ChEBI	L-proline	+	growth
22950	17115 ChEBI	L-serine	+	growth
22950	24996 ChEBI	lactate	+	growth
22950	25115 ChEBI	malate	+	growth
22950	15792 ChEBI	malonate	+	growth
22950	17306 ChEBI	maltose	+	growth
22950	29864 ChEBI	mannitol	-	growth
22950	37684 ChEBI	mannose	+	growth
22950	28053 ChEBI	melibiose	-	growth
22950	17268 ChEBI	myo-inositol	-	growth
22950	506227 ChEBI	N-acetyl-D-glucosamine	+	growth
22950	17632 ChEBI	nitrate	+	reduction
120490	17632 ChEBI	nitrate	-	reduction
22950	16301 ChEBI	nitrite	+	reduction
120490	16301 ChEBI	nitrite	-	reduction
22950	18401 ChEBI	phenylacetate	-	growth
22950	17272 ChEBI	propionate	+	growth
22950	17814 ChEBI	salicin	-	growth
22950	76282 ChEBI	suberate	-	growth
22950	17992 ChEBI	sucrose	+	growth
22950	16199 ChEBI	urea	+	hydrolysis
22950	31011 ChEBI	valerate	+	growth

Metabolite production

@ref	Chebi-ID	Metabolite	Production
22950	35581 ChEBI	indole
120490	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
22950	arginine dihydrolase	+	3.5.3.6
68382	beta-galactosidase	-	3.2.1.23	from API zym
22950	beta-glucosidase	+	3.2.1.21
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
22950	catalase	+	1.11.1.6
120490	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
22950	cytochrome oxidase	-	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
22950	gelatinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120490	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
22950	urease	+	3.5.1.5
120490	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	butanoate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	95.45	21 of 22
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	methylglyoxal degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	lipid A biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	gluconeogenesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	purine metabolism	72.34	68 of 94
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	alanine metabolism	68.97	20 of 29
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	lipid metabolism	67.74	21 of 31
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	histidine metabolism	58.62	17 of 29
66794	non-pathway related	57.89	22 of 38
66794	tyrosine metabolism	57.14	8 of 14
66794	tryptophan metabolism	55.26	21 of 38
66794	arginine metabolism	54.17	13 of 24
66794	urea cycle	53.85	7 of 13
66794	glycolysis	52.94	9 of 17
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	heme metabolism	50	7 of 14
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	D-cycloserine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	ketogluconate metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	degradation of sugar alcohols	37.5	6 of 16
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	oxidative phosphorylation	29.67	27 of 91
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	biotin biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	degradation of hexoses	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9

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
120490	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Composting

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7196	compost	Daejeon city	Republic of Korea	KOR	Asia
60056	Compost consisting of cow dung and rice straw	near Daejeon City	Republic of Korea	KOR	Asia
67770	Compost consisting of cow dung and rice straw	near Daejeon City	Republic of Korea	KOR	Asia
67771	From compost		Republic of Korea	KOR	Asia
120490	Environment, Compost, cow dung and rice straw	Daejeon	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB166885 (>99% sequence identity) for Stenotrophomonas from Microbeatlas

Aquatic Samples	259
Soil Samples	101
Animal Samples	353
Plant Samples	55
Total Samples	768

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7196	1	Risk group (German classification) According to TRBA 466
120490	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	ASM143152v1 assembly for Stenotrophomonas koreensis DSM 17805	contig	GCA_001431525	266128.3	2671180796	266128	56.89

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7196	Stenotrophomonas koreensis gene for 16S rRNA, partial sequence	AB166885	1463		266128

GC content

@ref	GC-content (mol%)	Method
67770	66	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: ASM143152v1 assembly for Stenotrophomonas koreensis DSM 17805
NCBI: GCA_001431525

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.46	no
125439	motility	BacteriaNetⓘ	yes	86.59	no
125439	gram_stain	BacteriaNetⓘ	negative	97.96	no
125439	spore_formation	BacteriaNetⓘ	no	99.86	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Stenotrophomonas koreensis strain DSM 17805
PATRIC: 266128.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	96.00	yes
125438	spore-forming	spore-formingⓘ	no	89.98	no
125438	aerobic	aerobicⓘ	yes	79.69	yes
125438	thermophilic	thermophileⓘ	no	96.90	no
125438	flagellated	motile2+ⓘ	no	64.56	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Extra benefit of microalgae in raw piggery wastewater treatment: pathogen reduction.	Lee SA, Kim M, Kim HS, Ahn CY.	Microbiome	10.1186/s40168-022-01339-3	2022
Genetics	Characterization of three Stenotrophomonas strains isolated from different ecosystems and proposal of Stenotrophomonas mori sp. nov. and Stenotrophomonas lacuserhaii sp. nov.	Deng Y, Han XF, Jiang ZM, Yu LY, Li Y, Zhang YQ.	Front Microbiol	10.3389/fmicb.2022.1056762	2022
Phylogeny	Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field.	Kim HB, Srinivasan S, Sathiyaraj G, Quan LH, Kim SH, Bui TPN, Liang ZQ, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.014662-0	2009
Phylogeny	Stenotrophomonas koreensis sp. nov., isolated from compost in South Korea.	Yang HC, Im WT, Kang MS, Shin DY, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63826-0	2006

References

#7196	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17805
#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 )
#22950	Hee-Chan Yang, Wan-Taek Im, Myung Suk Kang, Do-Yun Shin, Sung-Taik Lee: Stenotrophomonas koreensis sp. nov., isolated from compost in South Korea. IJSEM 56: 81 - 84 2006 ( DOI 10.1099/ijs.0.63826-0 , PubMed 16403870 )
#37460	; Curators of the CIP;
#60056	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53887
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#120490	Collection of Institut Pasteur ; Curators of the CIP; CIP 109170
#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

Stenotrophomonas koreensis (DSM 17805, JCM 13256, KCTC 12211)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001431525

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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