Strain identifier
BacDive ID: 162120
Type strain: 
Species: Iodidimonas gelatinilytica
Strain history: S. Amachi Mie-1.
NCBI tax ID(s): 1236966 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162120
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Iodidimonas gelatinilytica JCM 17845 is a mesophilic, Gram-negative bacterium that was isolated from Surface seawater in Mie.
NCBI tax id
- NCBI tax id: 1236966
- Matching level: species
strain history
- @ref: 67770
- history: S. Amachi Mie-1.
doi: 10.13145/bacdive162120.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Iodidimonadales
- family: Iodidimonadaceae
- genus: Iodidimonas
- species: Iodidimonas gelatinilytica
- full scientific name: Iodidimonas gelatinilytica Iino et al. 2022
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Iodidimonadales
family: Iodidimonadaceae
genus: Iodidimonas
species: Iodidimonas gelatinilytica
full scientific name: Iodidimonas gelatinilytica Iino et al.
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 96.1 |
| 125439 | negative | 99 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 91.753 |
| 125439 | no | 98.6 |
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Surface seawater in Mie
- country: Japan
- origin.country: JPN
- continent: Asia
Sequence information
16S sequences
- @ref: 67770
- description: Iodidimonas gelatinilytica Mie-1 DNA, sequence26, whole genome shotgun sequence
- accession: BKCM01000026
- length: 5502
- database: nuccore
- NCBI tax ID: 1236966
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Kordiimonadales bacterium JCM 17845 strain Mie-1 | 1236967.3 | wgs | patric | 1236966 |
| 67770 | Iodidimonas gelatinilytica Mie-1 | GCA_008579145 | contig | ncbi | 1236966 |
GC content
- @ref: 67770
- GC-content: 55.28
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 73 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 77.4 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.6 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.1 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 91.528 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 91.753 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.337 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 92.846 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 69.358 | no |
External links
@ref: 67770
culture collection no.: JCM 17845, LMG 28662
literature
- topic: Phylogeny
- Pubmed-ID: 33761033
- title: Iodidimonas gelatinilytica sp. nov., aerobic iodide-oxidizing bacteria isolated from brine water and surface seawater.
- authors: Iino T, Oshima K, Hattori M, Ohkuma M, Amachi S
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-021-01546-2
- year: 2021
- mesh: Alphaproteobacteria, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids, *Iodides, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Seawater, Sequence Analysis, DNA, *Water
- topic2: Transcriptome
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/ | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |