Stenotrophomonas chelatiphaga (DSM 21508, CCUG 57178, VKM B-2486)

Name: Stenotrophomonas chelatiphaga (DSM 21508, CCUG 57178, VKM B-2486)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17568

Type strain

Strain Designation LPM-5

Culture col. no. DSM 21508 CCUG 57178 VKM B-2486 LPM-5

NCBI tax ID(s) 517011

Special Collections DSMZ CCUG

History <- Y. A. Trotsenko, Inst. Biochem. Physiol. Microorg., Pushchino, Russia; LPM-5 <- E.N. Kaparullina <- T. I. Chistyakova

Links

Stenotrophomonas chelatiphaga LPM-5 is an aerobe bacterium that was isolated from sewage sludge.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400160

VKM B-2486,DSM 21508,CCUG 57178

@ref 20215

Last LPSN update 2026-02-09 11:22:15

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Stenotrophomonas

Species Stenotrophomonas chelatiphaga

Full scientific name Stenotrophomonas chelatiphaga Kaparullina et al. 2010

BacDive ID	Other strains from **Stenotrophomonas chelatiphaga** (1)	Type strain
155201	S. chelatiphaga CCUG 56889

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.994
125439	negative	96.4

Colony morphology

61226

Incubation period2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15753	EDTA-MEDIUM (DSMZ Medium 463a)		Medium recipe at MediaDive	Name: EDTA-MEDIUM (DSMZ Medium 463a) Composition: MgSO4 x 7 H2O 1.0 g/l EDTA 0.5 g/l Na2HPO4 x 2 H2O 0.41 g/l CaCl2 x 2 H2O 0.4 g/l KH2PO4 0.26 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00012 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 6.8e-05 g/l H3BO3 6.2e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l alpha-lipoic acid 5e-05 g/l Vitamin B12 5e-05 g/l Pantothenic acid 5e-05 g/l Riboflavin 5e-05 g/l Nicotine amide 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 2.4e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l CuCl2 x 2 H2O 1.7e-05 g/l Pyridoxamine hydrochloride 1e-05 g/l HCl Distilled water
15753	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15753	positive	growth	28
61226	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
61226	aerobe
125439	obligate aerobe	99.8

Spore formation

@ref	Spore formation	Confidence
125439		95

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	acetate fermentation	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	starch degradation	100	10 of 10
66794	valine metabolism	100	9 of 9
66794	gluconeogenesis	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	purine metabolism	82.98	78 of 94
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	alanine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	tyrosine metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	tryptophan metabolism	71.05	27 of 38
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	cysteine metabolism	66.67	12 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	d-xylose degradation	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	lysine metabolism	61.9	26 of 42
66794	sulfate reduction	61.54	8 of 13
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	heme metabolism	57.14	8 of 14
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	non-pathway related	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	degradation of pentoses	50	14 of 28
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	catecholamine biosynthesis	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	phenol degradation	45	9 of 20
66794	arachidonic acid metabolism	44.44	8 of 18
66794	degradation of sugar alcohols	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	3-chlorocatechol degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	oxidative phosphorylation	38.46	35 of 91
66794	carnitine metabolism	37.5	3 of 8
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	degradation of sugar acids	28	7 of 25
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Sewage sludge

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
15753	sewage sludge		Tartarstan, Kazan City	Russia	RUS	Europe
61226	Sewage sludge	2005	Tatarstan,Kazan City	Russia	RUS	Europe

Taxonmaps

69479

Global distribution of 16S sequence EU573216 (>99% sequence identity) for Stenotrophomonas from Microbeatlas

Aquatic Samples	340
Soil Samples	455
Animal Samples	566
Plant Samples	1192
Total Samples	2553

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15753	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	ASM143153v1 assembly for Stenotrophomonas chelatiphaga DSM 21508	contig	GCA_001431535	517011.3	2713896757	517011	46.93

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15753	Stenotrophomonas chelatiphaga strain LPM-5 16S ribosomal RNA gene, partial sequence	EU573216	1454		517011
124043	Stenotrophomonas chelatiphaga strain DSM 21508 16S ribosomal RNA gene, partial sequence.	MW227638	1388		517011

GC content

@ref	GC-content (mol%)	Method
15753	68.3	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Stenotrophomonas chelatiphaga DSM 21508
NCBI: GCA_001431535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.00	no
125439	motility	BacteriaNetⓘ	yes	76.50	no
125439	gram_stain	BacteriaNetⓘ	negative	96.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Stenotrophomonas chelatiphaga strain DSM 21508
PATRIC: 517011.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.99	no
125438	anaerobic	anaerobicⓘ	no	97.82	yes
125438	spore-forming	spore-formingⓘ	no	88.95	no
125438	aerobic	aerobicⓘ	yes	86.32	yes
125438	thermophilic	thermophileⓘ	no	97.67	no
125438	flagellated	motile2+ⓘ	yes	63.42	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas.	Pena MM, Bhandari R, Bowers RM, Weis K, Newberry E, Wagner N, Pupko T, Jones JB, Woyke T, Vinatzer BA, Jacques MA, Potnis N.	Genome Biol Evol	10.1093/gbe/evae074	2024
	Characterization of microorganisms following dairy keeping quality tests in Québec	Richter M, Sanschagrin L, Labrie A, Sanchez Martinez AC, Jubinville E, Goulet-Beaulieu V, Dufour S, Labrie S, Jean J.	Int Dairy J		2025
	Significance of siderophore-producing cyanobacteria on enhancing iron uptake potentiality of maize plants grown under iron-deficiency.	Brick MB, Hussein MH, Mowafy AM, Hamouda RA, Ayyad AM, Refaay DA.	Microb Cell Fact	10.1186/s12934-024-02618-4	2025
Genetics	A Novel Podophage StenR_269 Suggests a New Family in the Class Caudoviricetes.	Yakubovskij VI, Morozova VV, Kozlova YN, Tikunov AY, Babkin IV, Bardasheva AV, Zhirakovskaya EV, Baykov IK, Kaverina GB, Tikunova NV.	Viruses	10.3390/v15122437	2023
Genetics	Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance.	Ulrich K, Kube M, Becker R, Schneck V, Ulrich A.	Front Microbiol	10.3389/fmicb.2021.687463	2021
	Diversity and Biomineralization Potential of the Epilithic Bacterial Communities Inhabiting the Oldest Public Stone Monument of Cluj-Napoca (Transylvania, Romania).	Andrei AS, Pausan MR, Tamas T, Har N, Barbu-Tudoran L, Leopold N, Banciu HL.	Front Microbiol	10.3389/fmicb.2017.00372	2017
	The Roles of Plant-Growth-Promoting Rhizobacteria (PGPR)-Based Biostimulants for Agricultural Production Systems.	Sun W, Shahrajabian MH, Soleymani A.	Plants (Basel)	10.3390/plants13050613	2024
	The decolorization and degradation of azo dyes by two Stenotrophomonas strains isolated from textile effluent (Tepetitla, Mexico).	Vilchis-Carmona JA, Rodriguez-Luna IC, Elufisan TO, Sanchez-Varela A, Bibbins-Martinez M, Rivera G, Paz-Gonzalez AD, Villalobos-Lopez MA, Guo X.	Braz J Microbiol	10.1007/s42770-021-00542-y	2021
Genetics	Quantitative real-time PCR assay for the rapid identification of the intrinsically multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia.	Fraser TA, Bell MG, Harris PNA, Bell SC, Bergh H, Nguyen TK, Kidd TJ, Nimmo GR, Sarovich DS, Price EP.	Microb Genom	10.1099/mgen.0.000307	2019
	Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices.	Xia Y, DeBolt S, Dreyer J, Scott D, Williams MA.	Front Plant Sci	10.3389/fpls.2015.00490	2015
Phylogeny	Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens.	Chopyk J, Chattopadhyay S, Kulkarni P, Claye E, Babik KR, Reid MC, Smyth EM, Hittle LE, Paulson JN, Cruz-Cano R, Pop M, Buehler SS, Clark PI, Sapkota AR, Mongodin EF.	Microbiome	10.1186/s40168-017-0235-0	2017
	Seasonal variation of bacterial endophytes in urban trees.	Shen SY, Fulthorpe R.	Front Microbiol	10.3389/fmicb.2015.00427	2015
	Linking Bacterial Endophytic Communities to Essential Oils: Clues from Lavandula angustifolia Mill.	Emiliani G, Mengoni A, Maida I, Perrin E, Chiellini C, Fondi M, Gallo E, Gori L, Maggini V, Vannacci A, Biffi S, Firenzuoli F, Fani R.	Evid Based Complement Alternat Med	10.1155/2014/650905	2014
	ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.	Gonzalez E, Pitre FE, Brereton NJB.	Environ Microbiol	10.1111/1462-2920.14632	2019
	Stenotrophomonas goyi sp. nov., a novel bacterium associated with the alga Chlamydomonas reinhardtii.	Torres MJ, Fakhimi N, Dubini A, Gonzalez-Ballester D.	F1000Res	10.12688/f1000research.134978.3	2023
Phylogeny	Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations.	Sanchez-Castro I, Ruiz-Fresneda MA, Bakkali M, Kampfer P, Glaeser SP, Busse HJ, Lopez-Fernandez M, Martinez-Rodriguez P, Merroun ML	Int J Syst Evol Microbiol	10.1099/ijsem.0.002016	2017
Phylogeny	Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus.	Handa Y, Tazato N, Nagatsuka Y, Koide T, Kigawa R, Sano C, Sugiyama J	Int J Syst Evol Microbiol	10.1099/ijsem.0.000843	2015
Phylogeny	Stenotrophomonas chelatiphaga sp. nov., a new aerobic EDTA-degrading bacterium.	Kaparullina E, Doronina N, Chistyakova T, Trotsenko Y	Syst Appl Microbiol	10.1016/j.syapm.2008.12.003	2009

References

#15753	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21508
#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 )
#61226	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57178
#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 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Stenotrophomonas chelatiphaga (DSM 21508, CCUG 57178, VKM B-2486)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001431535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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