Strain identifier
BacDive ID: 163835
Type strain: 
Species: Dankookia rubra
Strain history: T.-Y. Ahn; Dankook Univ., South Korea; WS-10.
NCBI tax ID(s): 1442381 (species)
version 9.3 (current version)
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/bacdive163835.20250331.9.3
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 | gram stain | confidence |
|---|---|---|
| 125438 | negative | 97.684 |
| 125439 | negative | 92.4 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 99.1
spore formation
- @ref: 125439
- spore formation: no
- confidence: 95.2
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
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Dankookia rubra strain JCM30602 | 1442381.3 | wgs | patric | 1442381 |
| 66792 | Dankookia rubra JCM30602 | 2836988040 | draft | img | 1442381 |
| 67770 | Dankookia rubra JCM30602 | GCA_004355005 | contig | ncbi | 1442381 |
GC content
- @ref: 67770
- GC-content: 72.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.684 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 91.448 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 83.552 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 78.24 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.211 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 71.836 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 95.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 54 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 92.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.1 |
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
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 69479 | João 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 beta | https://microbeatlas.org/ |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |