Strain identifier
BacDive ID: 162241
Type strain: 
Species: Bradyrhizobium sp.
Strain history: K. Satsuma 17-4.
NCBI tax ID(s): 1215384 (species)
version 9.2 (current version)
General
@ref: 67770
BacDive-ID: 162241
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Bradyrhizobium sp. JCM 18382 is a mesophilic, Gram-negative bacterium that was isolated from Riverbed sediment of Tonegawa River.
NCBI tax id
- NCBI tax id: 1215384
- Matching level: species
strain history
- @ref: 67770
- history: K. Satsuma 17-4.
doi: 10.13145/bacdive162241.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Nitrobacteraceae
- genus: Bradyrhizobium
- species: Bradyrhizobium sp.
- full scientific name: Bradyrhizobium Jordan 1982
synonyms
- @ref: 20215
- synonym: Agromonas
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Nitrobacteraceae
genus: Bradyrhizobium
species: Bradyrhizobium sp.
full scientific name: Bradyrhizobium sp.
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 94.269
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Riverbed sediment of Tonegawa River
- geographic location: Ibaraki Pref.
- country: Japan
- origin.country: JPN
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_843.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_582;98_669;99_843&stattab=map
- Last taxonomy: Bradyrhizobium
- 16S sequence: AB672634
- Sequence Identity:
- Total samples: 29181
- soil counts: 14338
- aquatic counts: 4833
- animal counts: 6732
- plant counts: 3278
Sequence information
16S sequences
- @ref: 67770
- description: Bradyrhizobium sp. 17-4 gene for 16S ribosomal RNA, partial sequence
- accession: AB672634
- length: 1376
- database: nuccore
- NCBI tax ID: 1215384
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bradyrhizobium sp. 17-4 JCM 18382 | GCA_001312945 | contig | ncbi | 1215384 |
| 66792 | Bradyrhizobium sp. 17-4 strain JCM 18382 | 1215384.3 | wgs | patric | 1215384 |
| 66792 | Bradyrhizobium sp. JCM 18382 | 2734481923 | draft | img | 1215384 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 94.269 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 90.329 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.867 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 84.626 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.076 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 76.63 | no |
External links
@ref: 67770
culture collection no.: JCM 18382
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 |