Strain identifier
BacDive ID: 164163
Type strain: 
Species: Gelidibacter japonicus
Strain history: H. Doi; Inst. of Microb. Chem., Japan; Bio7-1.
NCBI tax ID(s): 1962232 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 164163
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Gelidibacter japonicus JCM 31967 is a mesophilic, Gram-negative bacterium that was isolated from Seawater collected from the Inland Sea in Japan.
NCBI tax id
- NCBI tax id: 1962232
- Matching level: species
strain history
- @ref: 67770
- history: H. Doi; Inst. of Microb. Chem., Japan; Bio7-1.
doi: 10.13145/bacdive164163.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Gelidibacter
- species: Gelidibacter japonicus
- full scientific name: Gelidibacter japonicus Doi and Osawa 2021
@ref: 67770
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Gelidibacter
species: Gelidibacter japonicus
full scientific name: Gelidibacter japonicus Doi and Osawa
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.966
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 | no | 99.989 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Seawater collected from the Inland Sea (Setonaikai) in Japan
taxonmaps
- @ref: 69479
- File name: preview.99_141706.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_3169;97_70213;98_94157;99_141706&stattab=map
- Last taxonomy: Gelidibacter
- 16S sequence: LC341257
- Sequence Identity:
- Total samples: 623
- soil counts: 82
- aquatic counts: 157
- animal counts: 361
- plant counts: 23
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Gelidibacter sp. Bio7-1 gene for 16S ribosomal RNA, partial sequence | LC217875 | 1448 | ena | 1962232 |
| 67770 | Gelidibacter sp. Bio7-1 gene for 16S ribosomal RNA, partial sequence, clone: 48 | LC341257 | 1445 | ena | 1962232 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gelidibacter sp. Bio7-1 | 1962232.3 | wgs | patric | 1962232 |
| 67770 | Gelidibacter japonicus Bio7-1 | GCA_010725055 | scaffold | ncbi | 1962232 |
GC content
- @ref: 67770
- GC-content: 39.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 86.526 | no |
| gram-positive | no | 97.915 | no |
| anaerobic | no | 99.428 | no |
| aerobic | yes | 86.865 | no |
| halophile | no | 67.153 | no |
| spore-forming | no | 94.34 | no |
| glucose-util | yes | 87.53 | no |
| flagellated | no | 93.838 | no |
| thermophile | no | 99.693 | yes |
| glucose-ferment | no | 86.806 | no |
External links
@ref: 67770
culture collection no.: JCM 31967, LMG 30063
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 31098768 | Description of Gelidibacter japonicus sp. nov., isolated from the Inland Sea (Setonaikai) in Japan. | Doi H, Osawa I | Arch Microbiol | 10.1007/s00203-019-01668-2 | 2019 | Base Composition/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, *Flavobacteriaceae/classification/genetics/isolation & purification, Japan, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Phenotype |
| Phylogeny | 34196770 | Gelidibacter pelagius sp. nov., Isolated from Coastal Sediment. | Lun HY, Gao C, Shang DD, Gong Y, Du ZJ | Curr Microbiol | 10.1007/s00284-021-02591-w | 2021 | Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids, *Flavobacteriaceae/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Vitamin K 2 | Transcriptome |
| Phylogeny | 34309686 | Gelidibacter maritimus sp. nov., isolated from marine sediment. | Gao C, Lun HY, Shang DD, Cai M, Ye MQ, Du ZJ | Arch Microbiol | 10.1007/s00203-021-02478-1 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Flavobacteriaceae/genetics, Geologic Sediments, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Vitamin K 2 | 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/ | |
| 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 |