Name: Stenotrophomonas pavanii CCUG 59972
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17570

Type strain:

Species: Stenotrophomonas pavanii

Culture col. no.: CCUG 59972, DSM 25135, CBMAI 564, ICB 89, LMG 25348, CIP 111741

Strain history: CIP <- 2019, LMG <- 2009, S. Van Trappen, LMG <- 2008, P.L. Ramos, Sao Paulo Univ., Sao Paulo, Brazil <- H.R. Barbosa, Biomedical Sciences Inst., Sao Paulo Univ., Sao Paulo, Brazil: strain ICB 89

NCBI tax ID(s): 487698 (species)

SI-ID 363691

LMG 25348, CBMAI 564, DSM 25135, CCUG 59972, CIP 111741

Section

Stenotrophomonas pavanii CCUG 59972 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from stems of sugar cane .

Gram-negative
rod-shaped
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 pavanii**
	Full Scientific Name (LPSN)	Stenotrophomonas pavanii Ramos et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29715]	Gram stain	negative
[Ref.: #121642]	Gram stain	negative

[Ref.: #29715]	Cell shape	rod-shaped
[Ref.: #121642]	Cell shape	rod-shaped

[Ref.: #29715]	Motility	no
[Ref.: #121642]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17917]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #17917]

Culture medium growth

[Ref.: #17917]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17917]

Culture medium composition

expand / minimize

[Ref.: #121642]

Culture medium

CIP Medium 72

[Ref.: #121642]

Culture medium growth

[Ref.: #121642]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #17917]	growth	28 °C
[Ref.: #29715]	growth	20-37 °C
[Ref.: #29715]	optimum	28.5 °C

[Ref.: #17917]	Temperature range	mesophilic
[Ref.: #29715]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29715]			optimum	8.5
[Ref.: #29715]			growth	05-12

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29715]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29715]		NaCl		growth	0.7-3.0	%
[Ref.: #29715]		NaCl		optimum	1.85	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #29715]	citrate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29715]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #29715]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #29715]	tween 80 ChEBI	+	carbon source
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #29715]	catalase	+	1.11.1.6
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #29715]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #17917]	25469	-	-	-	-	-	+	+	+	+	-	+	-	+	+	-	-	-	+	+	-	+

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

[Ref.: #17917]	Sample type/isolated from	stems of sugar cane (Brazilian variety widely used in organic farming)
[Ref.: #17917]	Geographic location (country and/or sea, region)	Sao Francisco Sertaozinho
[Ref.: #17917]	Country	Brazil
[Ref.: #17917]	Country ISO 3 Code	BRA
[Ref.: #17917]	Continent	Middle and South America

[Ref.: #62173]	Sample type/isolated from	Sugarcane plant stem,organic cultivated
[Ref.: #62173]	Country	Brazil
[Ref.: #62173]	Country ISO 3 Code	BRA
[Ref.: #62173]	Continent	Middle and South America

[Ref.: #121642]	Sample type/isolated from	Sugarcane, Saccharum officinarum, stem
[Ref.: #121642]	Geographic location (country and/or sea, region)	Usina Sao Francisco Sertaozinho
[Ref.: #121642]	Country	Brazil
[Ref.: #121642]	Country ISO 3 Code	BRA
[Ref.: #121642]	Continent	Middle and South America
[Ref.: #121642]	Isolation date	2000-01-03
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Stem (Branch)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ641452 (>99% sequence identity) for Stenotrophomonas from Microbeatlas

Aquatic Samples	10099
Soil Samples	6245
Animal Samples	29572
Plant Samples	2260
Total Samples	48176

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

[Ref.: #17917]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121642]	Biosafety level	1	Risk group (French classification)

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.: #29715]	Stenotrophomonas pavanii strain ICB 89 16S ribosomal RNA gene, partial sequence	FJ748683	1483	GenBank	487698 tax ID
[Ref.: #17917]	Stenotrophomonas pavanii strain LMG 25348 16S ribosomal RNA gene, partial sequence	HQ641452	1497	ENA	487698 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Stenotrophomonas pavanii LMG 25348	GCA_900101175	scaffold	GenBank	487698 tax ID	*
[Ref.: #66792]	Stenotrophomonas pavanii DSM 25135	GCA_001431565	contig	GenBank	487698 tax ID	*
[Ref.: #66792]	Stenotrophomonas pavanii strain DSM 25135	487698.4	wgs	PATRIC	487698 tax ID	*
[Ref.: #66792]	Stenotrophomonas pavanii strain LMG 25348	487698.5	wgs	PATRIC	487698 tax ID	*
[Ref.: #66792]	Stenotrophomonas pavanii LMG 25348	2623620583	draft	JGI IMG/M	487698 tax ID	*
[Ref.: #66792]	Stenotrophomonas pavanii DSM 25135	2740892494	draft	JGI IMG/M	487698 tax ID	*

[Ref.: #17917]

GC-content

67.5 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Stenotrophomonas pavanii LMG 25348 NCBI: GCA_900101175.1
[Ref.: #69480]	motile	yes	85.926	yes
[Ref.: #69480]	flagellated	no	80.473	yes
[Ref.: #69480]	gram-positive	no	97.906	no
[Ref.: #69480]	anaerobic	no	98.163	no
[Ref.: #69480]	aerobic	yes	88.203	no
[Ref.: #69480]	halophile	no	93.963	no
[Ref.: #69480]	spore-forming	no	95.752	yes
[Ref.: #69480]	glucose-ferment	no	90.766	no
[Ref.: #69480]	thermophile	no	99.528	yes
[Ref.: #69480]	glucose-util	yes	86.747	no

Availability in culture collections External links

[Ref.: #17917]

Culture collection no.

CCUG 59972, DSM 25135, CBMAI 564, ICB 89, LMG 25348, CIP 111741

[Ref.: #86566]

SI-ID 363691

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isolation and molecular identification of landfill bacteria capable of growing on di-(2-ethylhexyl) phthalate and deteriorating PVC materials.	Latorre I, Hwang S, Montalvo-Rodriguez R	J Environ Sci Health A Tox Hazard Subst Environ Eng	10.1080/10934529.2012.707549	2012	*
Phylogeny	Screening for endophytic nitrogen-fixing bacteria in Brazilian sugar cane varieties used in organic farming and description of Stenotrophomonas pavanii sp. nov.	Ramos PL, Van Trappen S, Thompson FL, Rocha RCS, Barbosa HR, De Vos P, Moreira-Filho CA	Int J Syst Evol Microbiol	10.1099/ijs.0.019372-0	2010	*
Phylogeny	Stenotrophomonas cyclobalanopsidis sp. nov., isolated from the leaf spot disease of Cyclobalanopsis patelliformis.	Bian DR, Xue H, Piao CG, Li Y	Antonie Van Leeuwenhoek	10.1007/s10482-020-01453-y	2020	*
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	*

References

#17917

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25135

#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 )

#29715

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 #26098 (see below)

#62173 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59972

#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) .

#68369

Automatically annotated from API 20NE .

#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) .

#86566

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-ID363691.1 )

#121642 Collection of Institut Pasteur ; Curators of the CIP; CIP 111741

#26098

IJSEM 926 2011 ( DOI 10.1099/ijs.0.019372-0 , PubMed 20495025 )

* These data were automatically processed and therefore are not curated

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Stenotrophomonas pavanii LMG 25348

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