Strain identifier
BacDive ID: 17363
Type strain: 
Species: Vibrio variabilis
Strain Designation: R-40492
Strain history: <- LMG <- I. Cleenwerck, BCCM/LMG <- L. Chimetto, Universidade Estadual de Campinas, Brazil
NCBI tax ID(s): 990271 (species)
version 9.3 (current version)
General
@ref: 18169
BacDive-ID: 17363
DSM-Number: 26147
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Vibrio variabilis R-40492 is a mesophilic, Gram-negative bacterium that was isolated from mucus of the zoanthid Palythoa caribaeorum.
NCBI tax id
- NCBI tax id: 990271
- Matching level: species
strain history
- @ref: 18169
- history: <- LMG <- I. Cleenwerck, BCCM/LMG <- L. Chimetto, Universidade Estadual de Campinas, Brazil
doi: 10.13145/bacdive17363.20250331.9.3
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 variabilis
- full scientific name: Vibrio variabilis Chimetto et al. 2011
@ref: 18169
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Vibrio
species: Vibrio variabilis
full scientific name: Vibrio variabilis Chimetto et al. 2011
strain designation: R-40492
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 98.7 |
| 125438 | negative | 99 |
Culture and growth conditions
culture medium
- @ref: 18169
- name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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: 18169
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 98.3
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.1
Isolation, sampling and environmental information
isolation
- @ref: 18169
- sample type: mucus of the zoanthid Palythoa caribaeorum
- host species: Palythoa caribaeorum
- geographic location: São Paulo, São Sebastião Channel, Portinho Beach
- country: Brazil
- origin.country: BRA
- continent: Middle and South America
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Cnidaria (Corals)
Safety information
risk assessment
- @ref: 18169
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18169
- description: Vibrio variabilis strain R-40492 16S ribosomal RNA (16S rRNA) gene, partial sequence
- accession: GU929924
- length: 1328
- database: nuccore
- NCBI tax ID: 990271
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Vibrio variabilis CAIM 1454 | GCA_003263785 | contig | ncbi | 990271 |
| 66792 | Vibrio variabilis strain CAIM 1454 | 990271.12 | wgs | patric | 990271 |
GC content
- @ref: 18169
- GC-content: 46.3
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.121 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 57.969 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.862 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 99 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 89.381 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 79.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.7 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 98.3 |
External links
@ref: 18169
culture collection no.: DSM 26147, CAIM 1454, LMG 25438
straininfo link
- @ref: 86364
- straininfo: 361316
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21296931 | Vibrio variabilis sp. nov. and Vibrio maritimus sp. nov., isolated from Palythoa caribaeorum. | Chimetto LA, Cleenwerck I, Moreira APB, Brocchi M, Willems A, De Vos P, Thompson FL | Int J Syst Evol Microbiol | 10.1099/ijs.0.026997-0 | 2011 | Animals, Anthozoa/*microbiology, Bacterial Proteins/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Vibrio/*classification/genetics/*isolation & purification | Genetics |
| Phylogeny | 29090323 | Vibrio hannami sp. nov., Isolated from Seawater. | Lee GE, Im WT, Park JS | Curr Microbiol | 10.1007/s00284-017-1376-x | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Vibrio/classification/genetics/*isolation & purification/metabolism | Metabolism |
| Phylogeny | 33480834 | Vibrio agarilyticus sp. nov., an agar-digesting marine bacterium isolated from coastal seawater in Daya Bay (Guangdong, China). | Wang X, Guo F, Tian P, Yu S, Xue CX, Wang W, Xiao J, Niu W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004647 | 2021 | Agar/metabolism, Bacterial Typing Techniques, Base Composition, Bays, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vibrio/*classification/isolation & purification | Transcriptome |
| Phylogeny | 34874245 | Vibrio ulleungensis sp. nov., isolated from Mytilus coruscus. | Moon YL, Park JS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005136 | 2021 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mytilus/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, *Vibrio/classification/isolation & purification | Transcriptome |
| Phylogeny | 36269578 | Vibrio ostreae sp. nov., a novel gut bacterium isolated from a Yellow Sea oyster. | Muhammad N, Nguyen TTH, Lee YJ, Ko J, Avila F, Kim SG | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005586 | 2022 | Animals, Bacterial Typing Techniques, Base Composition, Cardiolipins, Catalase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleotides, *Ostreidae/microbiology, Phosphatidylethanolamines, Phospholipids/chemistry, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, *Vibrio/genetics/isolation & purification | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 18169 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26147) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26147 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 86364 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID361316.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |