Strain identifier

BacDive ID: 163835

Type strain: Yes

Species: Dankookia rubra

Strain history: T.-Y. Ahn; Dankook Univ., South Korea; WS-10.

NCBI tax ID(s): 1442381 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 67770

BacDive-ID: 163835

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

description: Dankookia rubra JCM 30602 is a mesophilic, Gram-negative bacterium that was isolated from Sediment of a shallow stream in Cheonan.

NCBI tax id

  • NCBI tax id: 1442381
  • Matching level: species

strain history

  • @ref: 67770
  • history: T.-Y. Ahn; Dankook Univ., South Korea; WS-10.

doi: 10.13145/bacdive163835.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Dankookia
  • species: Dankookia rubra
  • full scientific name: Dankookia rubra Kim et al. 2016

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Acetobacteraceae

genus: Dankookia

species: Dankookia rubra

full scientific name: Dankookia rubra Kim et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 97.684

Culture and growth conditions

culture temp

  • @ref: 67770
  • growth: positive
  • type: growth
  • temperature: 30

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Sediment of a shallow stream in Cheonan
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

taxonmaps

  • @ref: 69479
  • File name: preview.99_62974.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_266;96_11782;97_14265;98_17604;99_62974&stattab=map
  • Last taxonomy: Dankookia rubra subclade
  • 16S sequence: KF309177
  • Sequence Identity:
  • Total samples: 387
  • soil counts: 179
  • aquatic counts: 99
  • animal counts: 74
  • plant counts: 35

Sequence information

16S sequences

  • @ref: 67770
  • description: Dankookia rubra strain WS-10 16S ribosomal RNA gene, partial sequence
  • accession: KF309177
  • length: 1411
  • database: nuccore
  • NCBI tax ID: 1442381

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dankookia rubra strain JCM306021442381.3wgspatric1442381
66792Dankookia rubra JCM306022836988040draftimg1442381
67770Dankookia rubra JCM30602GCA_004355005contigncbi1442381

GC content

  • @ref: 67770
  • GC-content: 72.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno88no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.684no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.448no
69480spore-formingspore-formingAbility to form endo- or exosporesno83.552no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes78.24no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.211yes
69480flagellatedmotile2+Ability to perform flagellated movementyes71.836no

External links

@ref: 67770

culture collection no.: JCM 30602, KACC 18533

literature

  • topic: Phylogeny
  • Pubmed-ID: 27225458
  • title: Dankookia rubra gen. nov., sp. nov., an alphaproteobacterium isolated from sediment of a shallow stream.
  • authors: Kim WH, Kim DH, Kang K, Ahn TY
  • journal: J Microbiol
  • DOI: 10.1007/s12275-016-6054-3
  • year: 2016
  • mesh: Alphaproteobacteria/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Geologic Sediments/*microbiology, Phylogeny, Republic of Korea, Rivers/*microbiology
  • topic2: Metabolism

Reference

@idauthorstitledoi/url
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1