Cite this strain

Stenotrophomonas ginsengisoli (DSM 24757, KCTC 12539, NBRC 101154)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17569

Type strain

Strain Designation DCY-01

Culture col. no. DSM 24757 KCTC 12539 NBRC 101154 CCUG 59870 DCY-01

NCBI tax ID(s) 336566

Special Collections DSMZ CCUG KCTC Literature strains

Links

Name and taxonomic classification

Stenotrophomonas ginsengisoli DCY-01 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng filed.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence Bacteria

SI-ID 396574

DSM 24757

Last LPSN update 2024-12-09 10:45:02

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Stenotrophomonas

Species Stenotrophomonas ginsengisoli

Full scientific name Stenotrophomonas ginsengisoli Kim et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell shape
22949	negative	rod-shaped
67771	negative
125438	negative
125439	negative
125439

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17752	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)	Range
17752	positive	growth	28	mesophilic
22949	negative	growth	4
22949	negative	growth	42
62144	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
22949	NaCl	positive	growth	5 %(w/v)

Observation

67771

Observationquinones: Q-8

Spore formation

@ref	Spore formation	Confidence
125438		91.949
125439		99.5

Enzymes

@ref	Value	Activity	Ec
22949	acid phosphatase	-	3.1.3.2
22949	alkaline phosphatase	-	3.1.3.1
22949	arginine dihydrolase	+	3.5.3.6
22949	beta-glucosidase	+	3.2.1.21
22949	catalase	+	1.11.1.6
22949	esterase (C 4)	+/-
22949	gelatinase	+
22949	leucine arylamidase	+/-	3.4.11.1
22949	N-acetyl-beta-glucosaminidase	-	3.2.1.52
22949	naphthol-AS-BI-phosphohydrolase	+/-
22949	trypsin	-	3.4.21.4
22949	urease	+	3.5.1.5

Metabolite production

@ref	Chebi-ID	Metabolite	Production
22949	35581 ChEBI	indole

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
22949	16808 ChEBI	2-dehydro-D-gluconate	-	growth
22949	16193 ChEBI	3-hydroxybenzoate	-	growth
22949	37054 ChEBI	3-hydroxybutyrate	-	growth
22949	17879 ChEBI	4-hydroxybenzoate	-	growth
22949	58143 ChEBI	5-dehydro-D-gluconate	-	growth
22949	30089 ChEBI	acetate	+	growth
22949	17128 ChEBI	adipate	-	growth
22949	22599 ChEBI	arabinose	-	growth
22949	16947 ChEBI	citrate	+	growth
22949	17108 ChEBI	D-arabinose	+	builds acid from
22949	12936 ChEBI	D-galactose	-	builds acid from
22949	17634 ChEBI	D-glucose	+	growth
22949	16899 ChEBI	D-mannitol	-	growth
22949	16024 ChEBI	D-mannose	+/-	builds acid from
22949	16024 ChEBI	D-mannose	+/-	growth
22949	65327 ChEBI	D-xylose	+	builds acid from
22949	27689 ChEBI	decanoate	-	growth
22949	4853 ChEBI	esculin	+	hydrolysis
22949	5291 ChEBI	gelatin	+	hydrolysis
22949	24265 ChEBI	gluconate	+	builds acid from
22949	17234 ChEBI	glucose	-	builds acid from
22949	17240 ChEBI	itaconate	-	growth
22949	16977 ChEBI	L-alanine	+	growth
22949	15971 ChEBI	L-histidine	+	growth
22949	15589 ChEBI	L-malate	+	growth
22949	17203 ChEBI	L-proline	+	growth
22949	62345 ChEBI	L-rhamnose	-	growth
22949	17115 ChEBI	L-serine	+	growth
22949	17266 ChEBI	L-sorbose	-	builds acid from
22949	24996 ChEBI	lactate	-	growth
22949	15792 ChEBI	malonate	+	growth
22949	17306 ChEBI	maltose	+/-	builds acid from
22949	17306 ChEBI	maltose	+	growth
22949	74863 ChEBI	methyl beta-D-xylopyranoside	+/-	builds acid from
22949	17268 ChEBI	myo-inositol	-	growth
22949	506227 ChEBI	N-acetyl-D-glucosamine	+	growth
22949	18401 ChEBI	phenylacetate	-	growth
22949	17272 ChEBI	propionate	-	growth
22949	16634 ChEBI	raffinose	+/-	builds acid from
22949	33942 ChEBI	ribose	-	growth
22949	30911 ChEBI	sorbitol	-	growth
22949	76282 ChEBI	suberate	-	growth
22949	17992 ChEBI	sucrose	+	growth
22949	27082 ChEBI	trehalose	-	builds acid from
22949	16199 ChEBI	urea	+	hydrolysis
22949	31011 ChEBI	valerate	-	growth

Oxygen tolerance

@ref	Oxygen tolerance
62144	aerobe
67771	aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17752	soil of ginseng filed	Daejeon city	Republic of Korea	KOR	Asia
62144	Soil,ginseng field	Daejeon city,near Daechung Lake	Republic of Korea	KOR	Asia
67771	From soil, ginseng field		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB681398 (>99% sequence identity) for Stenotrophomonas ginsengisoli from Microbeatlas

Aquatic Samples	92
Soil Samples	42
Animal Samples	245
Plant Samples	8
Total Samples	387

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
17752	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
17752	65.58	high performance liquid chromatography (HPLC)
67771	65.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Stenotrophomonas ginsengisoli gene for 16S rRNA, partial sequence, strain: NBRC 101154	AB681398	1470		336566
17752	Stenotrophomonas ginsengisoli strain DCY01 16S ribosomal RNA gene, partial sequence	DQ109037	1467		336566

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Stenotrophomonas ginsengisoli DSM 24757	GCA_001431485	contig		336566
66792	Stenotrophomonas ginsengisoli strain DSM 24757	336566.3	wgs	PATRIC	336566
66792	Stenotrophomonas ginsengisoli DSM 24757	2713896759	draft	JGI IMG/M	336566

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Stenotrophomonas ginsengisoli DSM 24757
NCBI: GCA_001431485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	92.80	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	75.30	no

Predictions from Diaspora project based on:
Stenotrophomonas ginsengisoli strain DSM 24757
PATRIC: 336566.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.24	yes
125438	anaerobic	anaerobicⓘ	no	96.48	yes
125438	spore-forming	spore-formingⓘ	no	91.95	no
125438	aerobic	aerobicⓘ	yes	80.15	no
125438	thermophilic	thermophileⓘ	no	95.88	yes
125438	flagellated	motile2+ⓘ	yes	52.82	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
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

Straininfo Link

@ref	Straininfo	Culture collections
86564	396574	DSM 24757
86565	409761	CCUG 59870

Culture collection no.

Culture collection no.
DSM 24757
KCTC 12539
NBRC 101154
CCUG 59870
DCY-01

References

#17752	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24757
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#22949	Ho-Bin Kim, Sathiyaraj Srinivasan, Gayathri Sathiyaraj, Lin-Hu Quan, Se-Hwa Kim, Thi Phuong Nam Bui, Zhi-qi Liang, Yeon-Ju Kim, Deok-Chun Yang: Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field. IJSEM 60: 1522 - 1526 2010 ( DOI 10.1099/ijs.0.014662-0 , PubMed 19684314 )
#62144	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59870
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#86564	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-ID396574.1 )
#86565	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-ID409761.1 )
#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 .

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