Name: Stenotrophomonas humi R-32729
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17566

Type strain:

Species: Stenotrophomonas humi

Strain Designation: R-32729

Culture col. no.: DSM 18929, LMG 23959, CCUG 54881

Strain history: <- K. Heylen, Ghent Univ.; R-32729

NCBI tax ID(s): 405444 (species)

SI-ID 290571

LMG 23959, DSM 18929, CCUG 54881

Section

Stenotrophomonas humi R-32729 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

Gram-negative
motile
rod-shaped
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 humi**
	Full Scientific Name (LPSN)	Stenotrophomonas humi Heylen et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32152]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #32152]	Cell shape	rod-shaped

[Ref.: #32152]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %93.583

[Ref.: #32152]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7790]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #7790]

Culture medium growth

[Ref.: #7790]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7790]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7790]	growth	28 °C
[Ref.: #32152]	growth	15-37 °C
[Ref.: #32152]	optimum	26 °C
[Ref.: #60368]	growth	30 °C

[Ref.: #7790]	Temperature range	mesophilic
[Ref.: #32152]	Temperature range	mesophilic
[Ref.: #60368]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32152]			optimum	7.75
[Ref.: #32152]			growth	5-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #60368]

Oxygen tolerance

aerobe

[Ref.: #32152]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32152]		NaCl		growth	2.25	%
[Ref.: #32152]		NaCl		optimum	0.5-4	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32152]	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.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32152]	fructose ChEBI	+	carbon source
[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.: #32152]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #32152]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #32152]	mannose ChEBI	+	carbon source
[Ref.: #32152]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #32152]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[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.: #32152]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #32152]	catalase	+	1.11.1.6
[Ref.: #32152]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[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.: #7790]	23524	+	-	-	-	-	-	+	-	+	-	+	-	+	+	-	+	-	+	+	-	-

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

[Ref.: #7790]	Sample type/isolated from	soil
[Ref.: #7790]	Geographic location (country and/or sea, region)	Gent
[Ref.: #7790]	Country	Belgium
[Ref.: #7790]	Country ISO 3 Code	BEL
[Ref.: #7790]	Continent	Europe

[Ref.: #60368]	Sample type/isolated from	Soil,enrichment with ethanol and nitrate
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM403587 (>99% sequence identity) for Stenotrophomonas from Microbeatlas

Aquatic Samples	65
Soil Samples	83
Animal Samples	115
Plant Samples	31
Total Samples	294

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

[Ref.: #7790]

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.: #32152]	Stenotrophomonas humi partial 16S rRNA gene, type strain R-32729T	AM403587	1494	GenBank	405444 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Stenotrophomonas humi DSM 18929	GCA_001431415	contig	GenBank	405444 tax ID	*
[Ref.: #66792]	Stenotrophomonas humi strain DSM 18929	405444.3	wgs	PATRIC	405444 tax ID	*
[Ref.: #66792]	Stenotrophomonas humi DSM 18929	2713896756	draft	JGI IMG/M	405444 tax ID	*

[Ref.: #32152]

GC-content

64 mol%

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 humi strain DSM 18929 PATRIC: 405444.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Stenotrophomonas humi strain DSM 18929 PATRIC: 405444.3
[Ref.: #69480]	gram-positive	no	98.38	yes
[Ref.: #69480]	anaerobic	no	98.581	yes
[Ref.: #69480]	halophile	no	92.594	no
[Ref.: #69480]	spore-forming	no	95.371	yes
[Ref.: #69480]	glucose-util	yes	88.25	yes
[Ref.: #69480]	aerobic	yes	93.145	no
[Ref.: #69480]	flagellated	no	73.484	no
[Ref.: #69480]	motile	yes	90.151	yes
[Ref.: #69480]	thermophile	no	98.719	yes
[Ref.: #69480]	glucose-ferment	no	89.02	yes

Availability in culture collections External links

[Ref.: #7790]

Culture collection no.

DSM 18929, LMG 23959, CCUG 54881

[Ref.: #86561]

SI-ID 290571

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Stenotrophomonas daejeonensis sp. nov., isolated from sewage.	Lee M, Woo SG, Chae M, Shin MC, Jung HM, Ten LN	Int J Syst Evol Microbiol	10.1099/ijs.0.017780-0	2010	*
Phylogeny	Stenotrophomonas panacihumi sp. nov., isolated from soil of a ginseng field.	Yi H, Srinivasan S, Kim MK	J Microbiol	10.1007/s12275-010-0006-0	2010	*
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 terrae sp. nov. and Stenotrophomonas humi sp. nov., two nitrate-reducing bacteria isolated from soil.	Heylen K, Vanparys B, Peirsegaele F, Lebbe L, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.65044-0	2007	*

References

#7790

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18929

#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 )

#32152

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 #28395 (see below)

#60368 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54881

#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) .

#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 )

#86561

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-ID290571.1 )

#28395

IJSEM 2056 2007 ( DOI 10.1099/ijs.0.65044-0 , PubMed 17766871 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Stenotrophomonas humi in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Stenotrophomonas humi strain DSM 18929

Stenotrophomonas humi strain DSM 18929

Change proposal

Change proposal