Name: Stenotrophomonas chelatiphaga LPM-5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17568

Type strain:

Species: Stenotrophomonas chelatiphaga

Strain Designation: LPM-5

Culture col. no.: DSM 21508, CCUG 57178, VKM B-2486

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

NCBI tax ID(s): 517011 (species)

SI-ID 400160

DSM 21508, CCUG 57178

Other strains from Stenotrophomonas chelatiphaga

S. chelatiphaga CCUG 56889

Section

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

motile
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Stenotrophomonas*
	Species	**Stenotrophomonas chelatiphaga**
	Full Scientific Name (LPSN)	Stenotrophomonas chelatiphaga Kaparullina et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.98

[Ref.: #69480]	Motility	yes Confidence in %92.836

[Ref.: #61226]

Incubation period

2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15753]

Culture medium

EDTA-MEDIUM (DSMZ Medium 463a)

[Ref.: #15753]

Culture medium growth

[Ref.: #15753]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15753]

Culture medium composition

expand / minimize

[Ref.: #15753]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #15753]

Culture medium growth

[Ref.: #15753]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15753]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15753]			growth	28 °C
[Ref.: #61226]			growth	30 °C

[Ref.: #15753]	Temperature range	mesophilic
[Ref.: #61226]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #61226]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	oxidative phosphorylation	38.46	35 of 91
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #15753]	Sample type/isolated from	sewage sludge
[Ref.: #15753]	Geographic location (country and/or sea, region)	Tartarstan, Kazan City
[Ref.: #15753]	Country	Russia
[Ref.: #15753]	Country ISO 3 Code	RUS
[Ref.: #15753]	Continent	Europe

[Ref.: #61226]	Sample type/isolated from	Sewage sludge
[Ref.: #61226]	Sampling date	2005
[Ref.: #61226]	Geographic location (country and/or sea, region)	Tatarstan,Kazan City
[Ref.: #61226]	Country	Russia
[Ref.: #61226]	Country ISO 3 Code	RUS
[Ref.: #61226]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Sewage sludge

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15753]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15753]	Stenotrophomonas chelatiphaga strain LPM-5 16S ribosomal RNA gene, partial sequence	EU573216	1454	ENA	517011 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Stenotrophomonas chelatiphaga DSM 21508	GCA_001431535	contig	GenBank	517011 tax ID	*
[Ref.: #66792]	Stenotrophomonas chelatiphaga strain DSM 21508	517011.3	wgs	PATRIC	517011 tax ID	*
[Ref.: #66792]	Stenotrophomonas chelatiphaga DSM 21508	2713896757	draft	JGI IMG/M	517011 tax ID	*

[Ref.: #15753]

GC-content

68.3 mol%

thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Stenotrophomonas chelatiphaga strain DSM 21508 PATRIC: 517011.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Stenotrophomonas chelatiphaga strain DSM 21508 PATRIC: 517011.3
[Ref.: #69480]	gram-positive	no	98.318	no
[Ref.: #69480]	anaerobic	no	98.579	no
[Ref.: #69480]	halophile	no	93.815	no
[Ref.: #69480]	spore-forming	no	96.224	no
[Ref.: #69480]	glucose-util	yes	91.411	no
[Ref.: #69480]	aerobic	yes	92.889	yes
[Ref.: #69480]	thermophile	no	99.274	yes
[Ref.: #69480]	flagellated	no	87.597	no
[Ref.: #69480]	motile	yes	86.452	no
[Ref.: #69480]	glucose-ferment	no	90.765	no

Availability in culture collections External links

[Ref.: #15753]

Culture collection no.

DSM 21508, CCUG 57178, VKM B-2486

[Ref.: #86563]

SI-ID 400160

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86563

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID400160.1 )

* These data were automatically processed and therefore are not curated

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Stenotrophomonas chelatiphaga strain DSM 21508

Stenotrophomonas chelatiphaga strain DSM 21508

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