Strain identifier
BacDive ID: 132001
Type strain: 
Species: Vibrio sonorensis
Strain Designation: PP5(1)
Strain history: <- B. Gomez-Gil, CAIM <- H. Cabanillas-Beltrán, Centro de Investigación en Alimentación y Desarrollo A.C., Unidad Mazatlán, Mexico
NCBI tax ID(s): 1004316 (species)
version 8.1 (current version)
General
@ref: 23793
BacDive-ID: 132001
DSM-Number: 102190
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Vibrio sonorensis PP5 is a mesophilic, motile bacterium that was isolated from cultured oyster .
NCBI tax id
- NCBI tax id: 1004316
- Matching level: species
strain history
- @ref: 23793
- history: <- B. Gomez-Gil, CAIM <- H. Cabanillas-Beltrán, Centro de Investigación en Alimentación y Desarrollo A.C., Unidad Mazatlán, Mexico
doi: 10.13145/bacdive132001.20230509.8.1
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 sonorensis
- full scientific name: Vibrio sonorensis González-Castillo et al. 2017
@ref: 23793
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Vibrio
species: Vibrio sonorensis
full scientific name: Vibrio sonorensis González-Castillo et al. 2017
strain designation: PP5(1)
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.985 | |
| 69480 | 99.971 | negative |
Culture and growth conditions
culture medium
- @ref: 23793
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
- @ref: 23793
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.901 |
Isolation, sampling and environmental information
isolation
- @ref: 23793
- sample type: cultured oyster (Crassostrea gigas) (31° 19' 00'' N 113° 32' 13'' W)
- host species: Crassostrea gigas
- geographic location: Sonora state, Puerto Peñasco, Estero Morua
- country: Mexico
- origin.country: MEX
- continent: North America
- latitude: 31.3167
- longitude: -113.537
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Aquaculture |
| #Host | #Invertebrates (Other) | #Mollusca |
Safety information
risk assessment
- @ref: 23793
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 23793
- description: Vibrio sonorensis strain CAIM 1076 16S ribosomal RNA gene, partial sequence
- accession: JQ434114
- length: 1439
- database: ena
- NCBI tax ID: 1004316
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Vibrio sonorensis CAIM 1076 | GCA_001854765 | contig | ncbi | 1004316 |
| 66792 | Vibrio sonorensis strain CAIM 1076 | 1004316.4 | wgs | patric | 1004316 |
| 66792 | Vibrio sonorensis CAIM 1076 | 2791355475 | draft | img | 1004316 |
GC content
- @ref: 23793
- GC-content: 44.4
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 89.877 | no |
| flagellated | yes | 89.93 | no |
| gram-positive | no | 98.741 | no |
| anaerobic | no | 95.729 | no |
| aerobic | yes | 72.028 | no |
| halophile | no | 51.12 | no |
| spore-forming | no | 94.981 | no |
| thermophile | no | 99.533 | yes |
| glucose-util | yes | 87.356 | no |
| glucose-ferment | yes | 85.536 | no |
External links
@ref: 23793
culture collection no.: DSM 102190, CAIM 1076, CECT 9100
straininfo link
- @ref: 90387
- straininfo: 398569
literature
- topic: Phylogeny
- Pubmed-ID: 27465217
- title: Vibrio sonorensis sp. nov. isolated from a cultured oyster Crassostrea gigas.
- authors: Gonzalez-Castillo A, Enciso-Ibarra J, Dubert J, Romalde JL, Gomez-Gil B
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-016-0744-z
- year: 2016
- mesh: Animals, Aquaculture, Crassostrea/*microbiology, DNA, Bacterial, Genome, Bacterial, Molecular Typing, Phylogeny, RNA, Ribosomal, 16S, Vibrio/classification/*isolation & purification
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 23793 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102190 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102190) | |
| 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 | |
| 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 | |
| 90387 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID398569.1 |