Strain identifier

BacDive ID: 17561

Type strain: Yes

Species: Stenotrophomonas koreensis

Strain Designation: TR6-01

Strain history: CIP <- 2006, JCM <- 2005, W.T. Im, Korea Adv. Inst. Sci. and Technol., Daejon, Korea: strain TR6-01

NCBI tax ID(s): 266128 (species)

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General

@ref: 7196

BacDive-ID: 17561

DSM-Number: 17805

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

description: Stenotrophomonas koreensis TR6-01 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from compost.

NCBI tax id

  • NCBI tax id: 266128
  • Matching level: species

strain history

@refhistory
7196<- S.-T. Lee; TR6-01 <- W.-T. Im
67770W.-T. Im TR6-01.
67771<- ST Lee, KAIST
120490CIP <- 2006, JCM <- 2005, W.T. Im, Korea Adv. Inst. Sci. and Technol., Daejon, Korea: strain TR6-01

doi: 10.13145/bacdive17561.20250331.9.3

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 koreensis
  • full scientific name: Stenotrophomonas koreensis Yang et al. 2006

@ref: 7196

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas koreensis

full scientific name: Stenotrophomonas koreensis Yang et al. 2006

strain designation: TR6-01

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotilitycell shape
67771negative
125438negative98.5
125439negative99.3
12543990.1yes
120490negativenorod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7196TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
37460MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120490CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
120490CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
7196positivegrowth28
37460positivegrowth37
60056positivegrowth30-37
67770positivegrowth30
67771positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
60056aerobe
67771aerobe
120490obligate aerobe
125439obligate aerobe95.5

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.4

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
22950168082-dehydro-D-gluconate-growth
22950161933-hydroxybenzoate-growth
22950370543-hydroxybutyrate-growth
22950178794-hydroxybenzoate-growth
22950581435-dehydro-D-gluconate-growth
2295030089acetate+growth
2295017128adipate-growth
2295027689decanoate-growth
2295016947citrate+growth
2295017634D-glucose+growth
2295028053melibiose-growth
2295016988D-ribose-growth
2295017924D-sorbitol-growth
2295024996lactate+growth
229504853esculin+hydrolysis
229505291gelatin+hydrolysis
2295017234glucose-builds acid from
2295028087glycogen-growth
2295027570histidine+growth
2295017268myo-inositol-growth
2295017240itaconate-growth
2295016977L-alanine+growth
2295030849L-arabinose-growth
2295018287L-fucose-growth
2295017203L-proline+growth
2295017115L-serine+growth
2295025115malate+growth
2295015792malonate+growth
2295017306maltose+growth
2295029864mannitol-growth
2295037684mannose+growth
22950506227N-acetyl-D-glucosamine+growth
2295018401phenylacetate-growth
2295017272propionate+growth
2295017814salicin-growth
2295076282suberate-growth
2295017992sucrose+growth
2295016199urea+hydrolysis
2295031011valerate+growth
2295017632nitrate+reduction
2295016301nitrite+reduction
12049017632nitrate-reduction
12049016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2295035581indoleno
12049035581indoleno

enzymes

@refvalueactivityec
22950arginine dihydrolase+3.5.3.6
22950beta-glucosidase+3.2.1.21
22950catalase+1.11.1.6
22950gelatinase+
22950cytochrome oxidase-1.9.3.1
22950urease+3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
120490oxidase+
120490catalase+1.11.1.6
120490urease-3.5.1.5
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-galactosidase-3.2.1.22
68382leucine arylamidase+3.4.11.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120490-+++-+--+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7196compostDaejeon cityRepublic of KoreaKORAsia
60056Compost consisting of cow dung and rice strawnear Daejeon CityRepublic of KoreaKORAsia
67770Compost consisting of cow dung and rice strawnear Daejeon CityRepublic of KoreaKORAsia
67771From compostRepublic of KoreaKORAsia
120490Environment, Compost, cow dung and rice strawDaejeonRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Biodegradation
  • Cat3: #Composting

taxonmaps

  • @ref: 69479
  • File name: preview.99_2232.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_1429;98_1740;99_2232&stattab=map
  • Last taxonomy: Stenotrophomonas
  • 16S sequence: AB166885
  • Sequence Identity:
  • Total samples: 768
  • soil counts: 101
  • aquatic counts: 259
  • animal counts: 353
  • plant counts: 55

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71961Risk group (German classification)
1204901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7196
  • description: Stenotrophomonas koreensis gene for 16S rRNA, partial sequence
  • accession: AB166885
  • length: 1463
  • database: nuccore
  • NCBI tax ID: 266128

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas koreensis strain DSM 17805266128.3wgspatric266128
66792Stenotrophomonas koreensis DSM 178052671180796draftimg266128
67770Stenotrophomonas koreensis DSM 17805GCA_001431525contigncbi266128

GC content

  • @ref: 67770
  • GC-content: 66
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.996yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.983no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.69yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.904no
125438motile2+flagellatedAbility to perform flagellated movementno64.562no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.4
125439BacteriaNetmotilityAbility to perform movementyes90.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.5

External links

@ref: 7196

culture collection no.: DSM 17805, JCM 13256, KCTC 12211, CCUG 53887, CIP 109170

straininfo link

  • @ref: 86557
  • straininfo: 232745

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16403870Stenotrophomonas koreensis sp. nov., isolated from compost in South Korea.Yang HC, Im WT, Kang MS, Shin DY, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63826-02006Fatty Acids, Korea, Molecular Sequence Data, RNA, Bacterial, RNA, Ribosomal, 16S, Sequence Homology, Nucleic Acid, *Soil, *Soil Microbiology, Species Specificity, Stenotrophomonas/chemistry/*classification/isolation & purification/physiologyGenetics
Phylogeny19684314Stenotrophomonas 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 DCInt J Syst Evol Microbiol10.1099/ijs.0.014662-02009Fatty Acids/analysis, Nucleic Acid Hybridization, Panax/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Stenotrophomonas/*classification/genetics/isolation & purificationPhenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7196Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17805)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17805
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
22950Hee-Chan Yang, Wan-Taek Im, Myung Suk Kang, Do-Yun Shin, Sung-Taik Lee10.1099/ijs.0.63826-0Stenotrophomonas koreensis sp. nov., isolated from compost in South KoreaIJSEM 56: 81-84 200616403870
37460Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6881
60056Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53887)https://www.ccug.se/strain?id=53887
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
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
86557Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232745.1StrainInfo: A central database for resolving microbial strain identifiers
120490Curators of the CIPCollection of Institut Pasteur (CIP 109170)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109170
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1