Strain identifier

BacDive ID: 17450

Type strain: Yes

Species: Dokdonella koreensis

Strain Designation: DS-123

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 323415 (species)

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General

@ref: 6813

BacDive-ID: 17450

DSM-Number: 17203

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

description: Dokdonella koreensis DS-123 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 323415
  • Matching level: species

strain history

@refhistory
6813<- J.-H. Yoon; DS-123
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive17450.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Dokdonella
  • species: Dokdonella koreensis
  • full scientific name: Dokdonella koreensis Yoon et al. 2006

@ref: 6813

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Rhodanobacteraceae

genus: Dokdonella

species: Dokdonella koreensis

full scientific name: Dokdonella koreensis Yoon et al. 2006

strain designation: DS-123

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31556negative01-02 µm0.3-0.5 µmrod-shapedyes
67771negative

pigmentation

  • @ref: 31556
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6813
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6813positivegrowth28mesophilic
31556positivegrowth10-39
31556positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31556positivegrowth05-09alkaliphile
31556positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31556aerobe
67771aerobe

spore formation

  • @ref: 31556
  • spore formation: no

observation

@refobservation
31556aggregates in chains
67771quinones: Q-8

metabolite utilization

  • @ref: 31556
  • Chebi-ID: 15361
  • metabolite: pyruvate
  • utilization activity: +
  • kind of utilization tested: carbon source

enzymes

@refvalueactivityec
31556catalase+1.11.1.6
31556cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6813soilDokdoRepublic of KoreaKORAsia
67771From soilDokdoRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2405.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_1296;97_1540;98_1875;99_2405&stattab=map
  • Last taxonomy: Dokdonella koreensis subclade
  • 16S sequence: AY987368
  • Sequence Identity:
  • Total samples: 2752
  • soil counts: 533
  • aquatic counts: 1601
  • animal counts: 536
  • plant counts: 82

Safety information

risk assessment

  • @ref: 6813
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6813
  • description: Dokdonella koreensis strain DS-123 16S ribosomal RNA gene, partial sequence
  • accession: AY987368
  • length: 1494
  • database: ena
  • NCBI tax ID: 323415

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dokdonella koreensis DS-123GCA_001632775completencbi1300342
66792Dokdonella koreensis DS-1231300342.5completepatric1300342
66792Dokdonella koreensis DS-1232687453174completeimg1300342

GC content

@refGC-content
681371.0
3155671

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.306no
gram-positiveno98.752yes
anaerobicno99.566no
aerobicyes94.333yes
halophileno94.218no
spore-formingno97.342yes
glucose-utilyes69.978no
motileno79.629no
thermophileno98.883yes
glucose-fermentno90.595no

External links

@ref: 6813

culture collection no.: DSM 17203, KCTC 12396

straininfo link

  • @ref: 86446
  • straininfo: 289858

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16403879Dokdonella koreensis gen. nov., sp. nov., isolated from soil.Yoon JH, Kang SJ, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63802-02006Base Composition, Cardiolipins, Gammaproteobacteria/chemistry/*classification/isolation & purification/physiology, Korea, Lipids, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19567557Dokdonella soli sp. nov., a gammaproteobacterium isolated from soil.Yoo SH, Weon HY, Anandham R, Kim BY, Hong SB, Jeon YA, Koo BS, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.005348-02009Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny19567572Dokdonella ginsengisoli sp. nov., isolated from soil from a ginseng field, and emended description of the genus Dokdonella.Ten LN, Jung HM, Im WT, Oh HW, Yang DC, Yoo SA, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.004945-02009Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny22863988Metallibacterium scheffleri gen. nov., sp. nov., an alkalinizing gammaproteobacterium isolated from an acidic biofilm.Ziegler S, Waidner B, Itoh T, Schumann P, Spring S, Gescher JInt J Syst Evol Microbiol10.1099/ijs.0.042986-02012Bacterial Typing Techniques, Base Composition, Biofilms, Cytochromes/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Iron, *Mining, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfides, Ubiquinone/analysis, Xanthomonadaceae/*classification/genetics/isolation & purificationGenetics
Phylogeny22888194Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent.Liu Y, Jin JH, Liu HC, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.042002-02012Bacterial Typing Techniques, Base Composition, Coloring Agents/metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Trityl Compounds/*metabolism, *Waste Disposal, Fluid, Xanthomonadaceae/*classification/genetics/isolation & purification/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6813Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17203)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17203
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
31556Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2784628776041
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
86446Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289858.1StrainInfo: A central database for resolving microbial strain identifiers