Strain identifier
BacDive ID: 162388
Type strain: 
Species: Geomicrobium sp.
Strain history: T. Kudo U326.
NCBI tax ID(s): 1460649 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 162388
keywords: genome sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Geomicrobium sp. JCM 19055 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from Sea cucumber .
NCBI tax id
- NCBI tax id: 1460649
- Matching level: species
strain history
- @ref: 67770
- history: T. Kudo U326.
doi: 10.13145/bacdive162388.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Geomicrobium
- species: Geomicrobium sp.
- full scientific name: Geomicrobium Echigo et al. 2010
@ref: 67770
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Caryophanales
family: Bacillaceae
genus: Geomicrobium
species: Geomicrobium sp.
full scientific name: Geomicrobium sp.
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 69480 | positive | 100 | |
| 69480 | 92.817 | yes |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | yes | 99.447 |
| 69481 | yes | 92 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Sea cucumber (Apostichopus japonicus)
- host species: Apostichopus japonicus
- geographic location: Omura Bay, Nagasaki
- country: Japan
- origin.country: JPN
- continent: Asia
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geomicrobium sp. JCM 19055 | 1460649.3 | wgs | patric | 1460649 |
| 66792 | Geomicrobium sp. JCM 19055 | 2619619137 | draft | img | 1460649 |
| 67770 | Geomicrobium sp. JCM 19055 | GCA_000698185 | contig | ncbi | 1460649 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 92 | no |
| motile | yes | 86.191 | no |
| gram-positive | yes | 86.057 | no |
| anaerobic | no | 98.722 | no |
| halophile | yes | 89.521 | no |
| spore-forming | yes | 83.587 | no |
| thermophile | no | 99.099 | no |
| glucose-util | yes | 84.236 | no |
| aerobic | yes | 93.388 | no |
| flagellated | yes | 55.663 | no |
| glucose-ferment | no | 93.043 | no |
External links
@ref: 67770
culture collection no.: JCM 19055
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/ | |
| 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 |