Strain identifier

BacDive ID: 17451

Type strain: Yes

Species: Dokdonella ginsengisoli

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 363846 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7287

BacDive-ID: 17451

DSM-Number: 17954

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

description: Dokdonella ginsengisoli DSM 17954 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil from a ginseng field.

NCBI tax id

  • NCBI tax id: 363846
  • Matching level: species

strain history

@refhistory
7287<- S. T. Lee, KAIST; Gsoil 191 <- W.-T. Im
67771<- ST Lee, KAIST

doi: 10.13145/bacdive17451.20230509.8.1

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 ginsengisoli
  • full scientific name: Dokdonella ginsengisoli Ten et al. 2009

@ref: 7287

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Rhodanobacteraceae

genus: Dokdonella

species: Dokdonella ginsengisoli

full scientific name: Dokdonella ginsengisoli Ten et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
29050negativerod-shapedno
67771negative

pigmentation

  • @ref: 29050
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7287
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7287positivegrowth30mesophilic
29050positivegrowth15-42
29050positiveoptimum30mesophilic
59556positivegrowth30-37mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29050positivegrowth5.75-9.75alkaliphile
29050positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29050aerobe
59556aerobe
67771aerobe

spore formation

  • @ref: 29050
  • spore formation: no

halophily

  • @ref: 29050
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2905030089acetate+carbon source
2905022599arabinose+carbon source
2905022653asparagine+carbon source
2905035391aspartate+carbon source
2905028757fructose+carbon source
2905017234glucose+carbon source
2905029987glutamate+carbon source
2905024996lactate+carbon source
2905026271proline+carbon source
2905017822serine+carbon source
2905016296D-tryptophan+carbon source
2905031011valerate+carbon source
2905018222xylose+carbon source
290504853esculin+hydrolysis

enzymes

@refvalueactivityec
29050catalase+1.11.1.6
29050gelatinase+
29050cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7287soil from a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
59556Soil,ginseng fieldPocheonRepublic of KoreaKORAsia
67771From soil of a ginseng field in Pocheon ProvinceRepublic 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_83458.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_1296;97_12480;98_15359;99_83458&stattab=map
  • Last taxonomy: Dokdonella ginsengisoli
  • 16S sequence: AB245362
  • Sequence Identity:
  • Total samples: 29
  • soil counts: 15
  • aquatic counts: 4
  • animal counts: 3
  • plant counts: 7

Safety information

risk assessment

  • @ref: 7287
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7287
  • description: Dokdonella ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 191
  • accession: AB245362
  • length: 1473
  • database: ena
  • NCBI tax ID: 363846

GC content

@refGC-contentmethod
728768.7high performance liquid chromatography (HPLC)
2905068.7

External links

@ref: 7287

culture collection no.: DSM 17954, CCUG 52462, KCTC 12564, Gsoil 191

straininfo link

  • @ref: 86447
  • straininfo: 404600

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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
7287Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17954)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17954
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
29050Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2548028776041
59556Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52462)https://www.ccug.se/strain?id=52462
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
86447Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404600.1StrainInfo: A central database for resolving microbial strain identifiers