Strain identifier
BacDive ID: 164441
Type strain: 
Species: Geomonas oryzae
Strain history: Y. Masuda and Z. Xu; Grad. Sch. of Agric. & Life Sci., Univ. of Tokyo, Japan; S43.
NCBI tax ID(s): 2364273 (species)
General
@ref: 67770
BacDive-ID: 164441
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative
description: Geomonas oryzae JCM 33030 is an anaerobe, Gram-negative bacterium that was isolated from Paddy field soil from Nagaoka.
NCBI tax id
- NCBI tax id: 2364273
- Matching level: species
strain history
- @ref: 67770
- history: Y. Masuda and Z. Xu; Grad. Sch. of Agric. & Life Sci., Univ. of Tokyo, Japan; S43.
doi: 10.13145/bacdive164441.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfuromonadales
- family: Geobacteraceae
- genus: Geomonas
- species: Geomonas oryzae
- full scientific name: Geomonas oryzae Xu et al. 2020
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfuromonadales
family: Geobacteraceae
genus: Geomonas
species: Geomonas oryzae
full scientific name: Geomonas oryzae
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 96.959
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-8
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Paddy field soil from Nagaoka
- geographic location: Niigata
- country: Japan
- origin.country: JPN
- continent: Asia
Sequence information
16S sequences
- @ref: 67770
- description: Geomonas oryzae strain S43 16S ribosomal RNA gene, partial sequence
- accession: MH915553
- length: 1424
- database: nuccore
- NCBI tax ID: 2364273
Genome sequences
- @ref: 67770
- description: Geomonas oryzae S43
- accession: GCA_004117875
- assembly level: contig
- database: ncbi
- NCBI tax ID: 2364273
GC content
- @ref: 67770
- GC-content: 61.2
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.959 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 70.151 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 77.359 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 78.722 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 92.762 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 69.114 | no |
External links
@ref: 67770
culture collection no.: JCM 33030, MCCC 1K03691
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 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 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 |