Strain identifier
BacDive ID: 162374
Type strain: 
Species: Geomicrobium sp.
Strain history: T. Kudo F414.
NCBI tax ID(s): 1460636 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 162374
keywords: genome sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Geomicrobium sp. JCM 19039 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from Sword-tail newt .
NCBI tax id
- NCBI tax id: 1460636
- Matching level: species
strain history
- @ref: 67770
- history: T. Kudo F414.
doi: 10.13145/bacdive162374.20230509.8.1
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 | 93.765 | 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 | 100 |
| 69481 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Sword-tail newt (Cynops ensicauda popei)
- host species: Cynops ensicauda popei
- geographic location: main island of Okinawa
- country: Japan
- origin.country: JPN
- continent: Asia
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geomicrobium sp. JCM 19039 | 1460636.3 | wgs | patric | 1460636 |
| 66792 | Geomicrobium sp. JCM 19039 | 2609460117 | draft | img | 1460636 |
| 67770 | Geomicrobium sp. JCM 19039 | GCA_000698145 | contig | ncbi | 1460636 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 85.111 | no |
| gram-positive | yes | 86.708 | no |
| anaerobic | no | 98.88 | no |
| halophile | yes | 89.112 | no |
| spore-forming | yes | 91.006 | no |
| glucose-util | yes | 89.217 | no |
| thermophile | no | 99.038 | yes |
| aerobic | yes | 94.018 | no |
| flagellated | yes | 50.939 | no |
| glucose-ferment | no | 91.538 | no |
External links
@ref: 67770
culture collection no.: JCM 19039
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 |