Strain identifier
BacDive ID: 17351
Type strain: 
Species: Vibrio owensii
Strain Designation: R-40496
Strain history: <- LMG <- I. Cleenwerck, University Ghent <- L. A. Chimetto, Institut de Biologia, Univ. Estadual de Campinas, Brazil; FR-233
NCBI tax ID(s): 1280004 (strain), 696485 (species)
version 9.1 (current version)
General
@ref: 17983
BacDive-ID: 17351
DSM-Number: 25291
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, motile, ovoid-shaped, animal pathogen
description: Vibrio owensii R-40496 is a Gram-negative, motile, ovoid-shaped animal pathogen that was isolated from mucus of the endemic coral Mussismilia hispida.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1280004 | strain |
| 696485 | species |
strain history
- @ref: 17983
- history: <- LMG <- I. Cleenwerck, University Ghent <- L. A. Chimetto, Institut de Biologia, Univ. Estadual de Campinas, Brazil; FR-233
doi: 10.13145/bacdive17351.20240916.9.1
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 owensii
- full scientific name: Vibrio owensii Cano-Gómez et al. 2010
synonyms
- @ref: 20215
- synonym: Vibrio communis
@ref: 17983
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Vibrio
species: Vibrio owensii
full scientific name: Vibrio owensii Cano-Gómez et al. 2010
strain designation: R-40496
type strain: no
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29735 | negative | 3 µm | 1 µm | ovoid-shaped | yes | |
| 69480 | negative | 100 |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 17983 | VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) | yes | https://mediadive.dsmz.de/medium/115 | Name: VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) Composition: NaCl 15.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
| 17983 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 | growth | type | temperature |
|---|---|---|---|
| 17983 | positive | growth | 28 |
| 29735 | positive | growth | 07-42 |
| 29735 | positive | optimum | 26 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
halophily
- @ref: 29735
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 3.75 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29735 | 21217 | L-alaninamide | + | carbon source |
| 29735 | 16449 | alanine | + | carbon source |
| 29735 | 40585 | alpha-cyclodextrin | + | carbon source |
| 29735 | 22653 | asparagine | + | carbon source |
| 29735 | 35391 | aspartate | + | carbon source |
| 29735 | 17057 | cellobiose | + | carbon source |
| 29735 | 23652 | dextrin | + | carbon source |
| 29735 | 28757 | fructose | + | carbon source |
| 29735 | 24265 | gluconate | + | carbon source |
| 29735 | 17234 | glucose | + | carbon source |
| 29735 | 29987 | glutamate | + | carbon source |
| 29735 | 17754 | glycerol | + | carbon source |
| 29735 | 28087 | glycogen | + | carbon source |
| 29735 | 17596 | inosine | + | carbon source |
| 29735 | 24996 | lactate | + | carbon source |
| 29735 | 17306 | maltose | + | carbon source |
| 29735 | 29864 | mannitol | + | carbon source |
| 29735 | 37684 | mannose | + | carbon source |
| 29735 | 51850 | methyl pyruvate | + | carbon source |
| 29735 | 506227 | N-acetylglucosamine | + | carbon source |
| 29735 | 17992 | sucrose | + | carbon source |
| 29735 | 26986 | threonine | + | carbon source |
| 29735 | 17748 | thymidine | + | carbon source |
| 29735 | 27082 | trehalose | + | carbon source |
| 29735 | 53423 | tween 40 | + | carbon source |
| 29735 | 53426 | tween 80 | + | carbon source |
| 29735 | 16704 | uridine | + | carbon source |
| 29735 | 17632 | nitrate | + | reduction |
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 17306 | maltose | + | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 16024 | D-mannose | + | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | + | hydrolysis |
| 68369 | 4853 | esculin | + | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | + | fermentation |
| 68369 | 27897 | tryptophan | + | energy source |
| 68369 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29735 | acid phosphatase | + | 3.1.3.2 |
| 29735 | alkaline phosphatase | + | 3.1.3.1 |
| 29735 | alpha-galactosidase | + | 3.2.1.22 |
| 29735 | catalase | + | 1.11.1.6 |
| 29735 | gelatinase | + | |
| 29735 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | + | |
| 68369 | beta-glucosidase | + | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 17983 | + | + | + | - | - | + | + | + | + | - | + | + | - | + | + | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 17983
- sample type: mucus of the endemic coral Mussismilia hispida
- host species: Mussismilia hispida
- geographic location: São Sebastião channel
- country: Brazil
- origin.country: BRA
- continent: Middle and South America
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Cnidaria (Corals)
taxonmaps
- @ref: 69479
- File name: preview.99_1344.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_74;98_81;99_1344&stattab=map
- Last taxonomy: Vibrio
- 16S sequence: GU078672
- Sequence Identity:
- Total samples: 345
- soil counts: 4
- aquatic counts: 169
- animal counts: 159
- plant counts: 13
Safety information
risk assessment
- @ref: 17983
- pathogenicity animal: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 29735 | Vibrio sp. LMG 20370 partial 16S rRNA gene, strain LMG 20370 | AJ345066 | 1470 | nuccore | 696485 |
| 17983 | Vibrio communis strain R-40496 16S ribosomal RNA gene, partial sequence | GU078672 | 1470 | nuccore | 696485 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Vibrio owensii LMG 25430 | GCA_000400325 | scaffold | ncbi | 1280004 |
| 66792 | Vibrio owensii LMG 25430 | 1280004.3 | wgs | patric | 1280004 |
| 66792 | Vibrio owensii LMG 25430 | 2568526433 | draft | img | 1280004 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17983 | 45.92 | sequence analysis |
| 29735 | 45.8 |
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 | 100 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.876 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 60.219 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 84.755 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 99 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 88.432 | no |
External links
@ref: 17983
culture collection no.: DSM 25291, CAIM 1816, LMG 25430
straininfo link
- @ref: 86352
- straininfo: 362408
literature
- topic: Phylogeny
- Pubmed-ID: 20305064
- title: Vibrio communis sp. nov., isolated from the marine animals Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis and Litopenaeus vannamei.
- authors: Chimetto LA, Cleenwerck I, Alves N, Silva BS, Brocchi M, Willems A, De Vos P, Thompson FL
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.019729-0
- year: 2010
- mesh: Amplified Fragment Length Polymorphism Analysis, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Brazil, DNA, Bacterial/genetics, Ecuador, Fatty Acids/analysis, Molecular Sequence Data, Multilocus Sequence Typing, Penaeidae/*microbiology, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/*classification/genetics/isolation & purification
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17983 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25291) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25291 | |||
| 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 | |||
| 29735 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26117 | 28776041 | |
| 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) | |||
| 68369 | Automatically annotated from API 20NE | |||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 86352 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID362408.1 | StrainInfo: A central database for resolving microbial strain identifiers |