Strain identifier

BacDive ID: 17569

Type strain: Yes

Species: Stenotrophomonas ginsengisoli

Strain Designation: DCY-01

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 336566 (species)

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General

@ref: 17752

BacDive-ID: 17569

DSM-Number: 24757

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

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

NCBI tax id

  • NCBI tax id: 336566
  • Matching level: species

strain history

@refhistory
17752<- KCTC <- D.-C. Yang, Kyung Hee Univ., Seoul, Republic of Korea
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive17569.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Stenotrophomonas
  • species: Stenotrophomonas ginsengisoli
  • full scientific name: Stenotrophomonas ginsengisoli Kim et al. 2010

@ref: 17752

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas ginsengisoli

full scientific name: Stenotrophomonas ginsengisoli Kim et al. 2010

strain designation: DCY-01

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
22949negativerod-shaped
67771negative
69480yes94.428
69480negative99.994

Culture and growth conditions

culture medium

  • @ref: 17752
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: 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

@refgrowthtypetemperaturerange
17752positivegrowth28mesophilic
22949nogrowth4psychrophilic
22949nogrowth42thermophilic
62144positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
62144aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

  • @ref: 22949
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 5 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
22949168082-dehydro-D-gluconate-growth
22949161933-hydroxybenzoate-growth
22949178794-hydroxybenzoate-growth
22949581435-dehydro-D-gluconate-growth
2294930089acetate+growth
2294917128adipate-growth
2294922599arabinose-growth
2294927689decanoate-growth
2294916947citrate+growth
2294917108D-arabinose+builds acid from
2294912936D-galactose-builds acid from
2294917634D-glucose+growth
2294916899D-mannitol-growth
2294916024D-mannose+/-builds acid from
2294916024D-mannose+/-growth
2294965327D-xylose+builds acid from
22949370543-hydroxybutyrate-growth
2294924996lactate-growth
229494853esculin+hydrolysis
229495291gelatin+hydrolysis
2294924265gluconate+builds acid from
2294917234glucose-builds acid from
2294917268myo-inositol-growth
2294917240itaconate-growth
2294916977L-alanine+growth
2294915971L-histidine+growth
2294915589L-malate+growth
2294917203L-proline+growth
2294962345L-rhamnose-growth
2294917115L-serine+growth
2294917266L-sorbose-builds acid from
2294915792malonate+growth
2294917306maltose+/-builds acid from
2294917306maltose+growth
2294974863methyl beta-D-xylopyranoside+/-builds acid from
22949506227N-acetyl-D-glucosamine+growth
2294918401phenylacetate-growth
2294917272propionate-growth
2294916634raffinose+/-builds acid from
2294933942ribose-growth
2294930911sorbitol-growth
2294976282suberate-growth
2294917992sucrose+growth
2294927082trehalose-builds acid from
2294916199urea+hydrolysis
2294931011valerate-growth

metabolite production

  • @ref: 22949
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17752soil of ginseng filedDaejeon cityRepublic of KoreaKORAsia
62144Soil,ginseng fieldDaejeon city,near Daechung LakeRepublic of KoreaKORAsia
67771From soil, ginseng fieldRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8287.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_288;98_6031;99_8287&stattab=map
  • Last taxonomy: Stenotrophomonas ginsengisoli
  • 16S sequence: AB681398
  • Sequence Identity:
  • Total samples: 387
  • soil counts: 42
  • aquatic counts: 92
  • animal counts: 245
  • plant counts: 8

Safety information

risk assessment

  • @ref: 17752
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Stenotrophomonas ginsengisoli gene for 16S rRNA, partial sequence, strain: NBRC 101154AB6813981470ena336566
17752Stenotrophomonas ginsengisoli strain DCY01 16S ribosomal RNA gene, partial sequenceDQ1090371467ena336566

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas ginsengisoli DSM 24757GCA_001431485contigncbi336566
66792Stenotrophomonas ginsengisoli strain DSM 24757336566.3wgspatric336566
66792Stenotrophomonas ginsengisoli DSM 247572713896759draftimg336566

GC content

@refGC-contentmethod
1775265.58high performance liquid chromatography (HPLC)
6777165.58

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.616no
anaerobicno96.454no
halophileno92.456no
spore-formingno95.438no
glucose-utilyes81.234no
motileyes91.543no
flagellatedno81.353no
thermophileno99.084no
aerobicyes86.816yes
glucose-fermentno91.688no

External links

@ref: 17752

culture collection no.: DSM 24757, KCTC 12539, NBRC 101154, CCUG 59870

straininfo link

@refstraininfo
86564396574
86565409761

literature

  • topic: Phylogeny
  • Pubmed-ID: 19684314
  • title: Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field.
  • authors: Kim HB, Srinivasan S, Sathiyaraj G, Quan LH, Kim SH, Bui TPN, Liang ZQ, Kim YJ, Yang DC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.014662-0
  • year: 2009
  • mesh: Fatty Acids/analysis, Nucleic Acid Hybridization, Panax/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Stenotrophomonas/*classification/genetics/isolation & purification
  • topic2: Phenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17752Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24757)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24757
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
22949Ho-Bin Kim, Sathiyaraj Srinivasan, Gayathri Sathiyaraj, Lin-Hu Quan, Se-Hwa Kim, Thi Phuong Nam Bui, Zhi-qi Liang, Yeon-Ju Kim, Deok-Chun Yang10.1099/ijs.0.014662-0Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng fieldIJSEM 60: 1522-1526 201019684314
62144Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59870)https://www.ccug.se/strain?id=59870
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86564Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396574.1StrainInfo: A central database for resolving microbial strain identifiers
86565Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID409761.1StrainInfo: A central database for resolving microbial strain identifiers