Strain identifier
BacDive ID: 162331
Type strain: 
Species: Vibrio sp.
Strain history: T. Kudo C141.
NCBI tax ID(s): 1298599 (species)
version 9.2 (current version)
General
@ref: 67770
BacDive-ID: 162331
keywords: genome sequence, Bacteria, mesophilic, Gram-negative
description: Vibrio sp. JCM 18904 is a mesophilic, Gram-negative bacterium that was isolated from Sea cucumber Holothuria leucospilota.
NCBI tax id
- NCBI tax id: 1298599
- Matching level: species
strain history
- @ref: 67770
- history: T. Kudo C141.
doi: 10.13145/bacdive162331.20241212.9.2
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Vibrionales
- family: Vibrionaceae
- genus: Vibrio
- species: Vibrio sp.
- full scientific name: Vibrio Pacini 1854 (Approved Lists 1980)
synonyms
@ref synonym 20215 Beneckea 20215 Lucibacterium 20215 Allomonas
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales
family: Vibrionaceae
genus: Vibrio
species: Vibrio sp.
full scientific name: Vibrio sp.
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Sea cucumber Holothuria leucospilota
- host species: Holothuria leucospilota
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Vibrio sp. JCM 18904 | GCA_001315185 | contig | ncbi | 1298599 |
| 66792 | Vibrio sp. JCM 18904 | 1298599.3 | wgs | patric | 1298599 |
| 66792 | Vibrio sp. JCM 18904 | 1298599.4 | wgs | patric | 1298599 |
| 66792 | Vibrio sp. JCM 18904 | 2579778626 | draft | img | 1298599 |
| 67770 | Vibrio sp. JCM 18904 | GCA_000695035 | contig | ncbi | 1298599 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.196 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.241 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 57.855 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 99.5 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 87.115 | no |
External links
@ref: 67770
culture collection no.: JCM 18904
literature
- topic: Genetics
- Pubmed-ID: 24948773
- title: Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod.
- authors: Kudo T, Kawauchi A, Nakahara T, Zhang X, Taniyama S, Takatani T, Arakawa O, Oshima K, Suda W, Kitamura K, Iida T, Iino T, Inoue T, Hongoh Y, Hattori M, Ohkuma M
- journal: Genome Announc
- DOI: 10.1128/genomeA.00623-14
- year: 2014
- topic2: Phylogeny
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 |