Strain identifier
BacDive ID: 161802
Type strain: 
Species: Variovorax sp.
Strain history: K. Satsuma RA8.
NCBI tax ID(s): 662548 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 161802
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Variovorax sp. JCM 16519 is a mesophilic, Gram-negative bacterium that was isolated from Sediment of the Kinugawa River.
NCBI tax id
- NCBI tax id: 662548
- Matching level: species
strain history
- @ref: 67770
- history: K. Satsuma RA8.
doi: 10.13145/bacdive161802.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Variovorax
- species: Variovorax sp.
- full scientific name: Variovorax Willems et al. 1991
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Variovorax
species: Variovorax sp.
full scientific name: Variovorax sp.
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.971
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 100 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Sediment of the Kinugawa River
- geographic location: Ibaraki Pref.
- country: Japan
- origin.country: JPN
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_2041.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_308;97_342;98_387;99_2041&stattab=map
- Last taxonomy: Variovorax
- 16S sequence: AB513921
- Sequence Identity:
- Total samples: 2299
- soil counts: 1409
- aquatic counts: 220
- animal counts: 220
- plant counts: 450
Sequence information
16S sequences
- @ref: 67770
- description: Variovorax sp. RA8 gene for 16S rRNA, partial sequence
- accession: AB513921
- length: 1526
- database: ena
- NCBI tax ID: 662548
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Variovorax sp. RA8 JCM 16519 | GCA_001312365 | contig | ncbi | 662548 |
| 66792 | Variovorax sp. RA8 strain JCM 16519 | 662548.6 | wgs | patric | 662548 |
| 66792 | Variovorax sp. JCM 16519 | 2728369721 | draft | img | 662548 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.258 | no |
| anaerobic | no | 99.099 | no |
| halophile | no | 93.922 | no |
| spore-forming | no | 93.609 | no |
| glucose-util | no | 51.583 | no |
| flagellated | no | 84.812 | no |
| thermophile | no | 99.357 | yes |
| motile | yes | 73.465 | no |
| aerobic | yes | 94.514 | no |
| glucose-ferment | no | 91.474 | no |
External links
@ref: 67770
culture collection no.: JCM 16519
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/ |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |