Strain identifier
BacDive ID: 17327
Type strain:
Species: Vibrio ordalii
Strain Designation: Dom F3 kid
Strain history: CIP <- 1988, NCIB <- 1981, M.H. Schiewe: strain Dom F3 kid <- E.J. Ordal
NCBI tax ID(s): 990998 (strain), 28174 (species)
General
@ref: 8213
BacDive-ID: 17327
DSM-Number: 19621
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, animal pathogen
description: Vibrio ordalii Dom F3 kid is an aerobe, mesophilic, motile animal pathogen that was isolated from kidney of moribund coho salmon .
NCBI tax id
NCBI tax id | Matching level |
---|---|
28174 | species |
990998 | strain |
strain history
@ref | history |
---|---|
8213 | <- CCUG <- CECT <- NCIMB <- M. H. Schiewe; DF3K <- E. J. Ordal |
121431 | CIP <- 1988, NCIB <- 1981, M.H. Schiewe: strain Dom F3 kid <- E.J. Ordal |
doi: 10.13145/bacdive17327.20230509.8.1
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 ordalii
- full scientific name: Vibrio ordalii Schiewe et al. 1982
@ref: 8213
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Vibrio
species: Vibrio ordalii
full scientific name: Vibrio ordalii Schiewe et al. 1982
strain designation: Dom F3 kid
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 97.657 | ||
69480 | 99.996 | negative | ||
121431 | yes | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8213 | MARINE BROTH (ROTH CP73) (DSMZ Medium 514f) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514f.pdf | |
41338 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
121431 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8213 | positive | growth | 28 | mesophilic |
41338 | positive | growth | 25 | mesophilic |
54249 | positive | growth | 26-30 | mesophilic |
121431 | positive | growth | 22-30 | |
121431 | no | growth | 37 | mesophilic |
121431 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 54249
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.99 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
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 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | + | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | + | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | - | fermentation |
68368 | 17634 | D-glucose | - | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
121431 | 17632 | nitrate | - | reduction |
121431 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
68369 | 35581 | indole | - | |
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | gelatinase | - | |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
68368 | cytochrome oxidase | + | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
121431 | oxidase | + | |
121431 | alcohol dehydrogenase | - | 1.1.1.1 |
121431 | catalase | + | 1.11.1.6 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121431 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8213 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8213 | - | - | + | - | - | - | - | + | + | - | - | + | - | - | - | - | - | - | - | - | + |
8213 | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121431 | + | + | - | - | - | - | - | + | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
8213 | kidney of moribund coho salmon (Oncorhyncus kisutch) | Oncorhyncus kisutch | Washington, Purget Sound | USA | USA | North America |
54249 | Kidney of moribund coho salmon,Oncorhyncus kisutch | Washington,Purget Sound | USA | USA | North America | |
121431 | Animal, Moribund coho salmon, kidney tissue | Washington | United States of America | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Fishes | #Salmonidae |
#Host Body-Site | #Urogenital tract | #Kidney |
taxonmaps
- @ref: 69479
- File name: preview.99_2159.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_361;98_1685;99_2159&stattab=map
- Last taxonomy: Vibrio anguillarum
- 16S sequence: X74718
- Sequence Identity:
- Total samples: 216
- soil counts: 5
- aquatic counts: 148
- animal counts: 63
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
8213 | yes | 1 | Risk group (German classification) |
121431 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Vibrio ordalii DNA, 16S-23S rRNA intergenic spacer, partial sequence, strain: ATCC 33509 | AB255727 | 260 | ena | 990998 |
20218 | Vibrio ordalii 16S rRNA | D11214 | 219 | ena | 28174 |
20218 | Vibrio ordalii 16S rRNA | D11263 | 214 | ena | 28174 |
20218 | Vibrio ordalii 16S rRNA | D11312 | 192 | ena | 28174 |
20218 | Vibrio ordalii strain ATCC 33509 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence | EU570972 | 598 | ena | 990998 |
20218 | Vibrio ordalii strain ATCC 33509 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer and tRNA-Ala gene, complete sequence; and 23S ribosomal RNA gene, partial sequence | EU570973 | 476 | ena | 990998 |
20218 | Vibrio ordalii strain ATCC 33509 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu, tRNA-Lys, and tRNA-Val genes, complete sequence | FJ666335 | 724 | ena | 990998 |
20218 | Vibrio ordalii strain ATCC 33509 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu, tRNA-Lys, tRNA-Ala, and tRNA-Val genes, complete sequence | FJ666336 | 821 | ena | 990998 |
8213 | V.ordalii gamma subclass (ATCC 33509) gene for 16S rRNA | X70641 | 1480 | ena | 990998 |
8213 | V.ordalii (ATCC 33509T) gene for 16S ribosomal RNA | X74718 | 1425 | ena | 990998 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Vibrio ordalii ATCC 33509 | 990998.3 | wgs | patric | 990998 |
66792 | Vibrio ordalii Schiewe DF3K, ATCC 33509 | 2513237346 | draft | img | 990998 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 89.586 | no |
flagellated | yes | 85.728 | no |
gram-positive | no | 99 | no |
anaerobic | no | 94.248 | yes |
halophile | no | 50 | no |
spore-forming | no | 95.677 | no |
thermophile | no | 98.703 | no |
glucose-util | yes | 89.27 | no |
aerobic | yes | 78.416 | no |
glucose-ferment | yes | 80.487 | yes |
External links
@ref: 8213
culture collection no.: DSM 19621, ATCC 33509, CCRC 12916, CCUG 38425, CECT 582, CIP 103205, NCIMB 2167
straininfo link
- @ref: 86327
- straininfo: 7461
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18429439 | Antigenic and molecular characterization of Vibrio ordalii strains isolated from Atlantic salmon Salmo salar in Chile. | Silva-Rubio A, Acevedo C, Magarinos B, Jaureguiberry B, Toranzo AE, Avendano-Herrera R | Dis Aquat Organ | 10.3354/dao01872 | 2008 | Animals, Antigens, Bacterial/analysis/immunology, Base Sequence, Blotting, Western, Chile, DNA Fingerprinting, Fish Diseases/*microbiology, Salmo salar/*microbiology, Sequence Homology, Nucleic Acid, Serotyping, Vibrio/classification/*genetics/*immunology/isolation & purification, Vibrio Infections/microbiology/*veterinary | Enzymology |
25667332 | Cell-surface properties of Vibrio ordalii strains isolated from Atlantic salmon Salmo salar in Chilean farms. | Ruiz P, Poblete M, Yanez AJ, Irgang R, Toranzo AE, Avendano-Herrera R | Dis Aquat Organ | 10.3354/dao02820 | 2015 | Animals, Bacterial Adhesion/physiology, Biofilms/growth & development, Cell Line, Chile/epidemiology, Fish Diseases/epidemiology/*microbiology, Mucus/microbiology, Oncorhynchus mykiss, *Salmo salar, Skin/microbiology, Vibrio/*cytology/pathogenicity/physiology, Vibrio Infections/epidemiology/microbiology/*veterinary, Virulence | ||
Genetics | 27382430 | The complete genome sequence and analysis of vB_VorS-PVo5, a Vibrio phage infectious to the pathogenic bacterium Vibrio ordalii ATCC-33509. | Echeverria-Vega A, Morales-Vicencio P, Saez-Saavedra C, Ceh J, Araya R | Stand Genomic Sci | 10.1186/s40793-016-0166-6 | 2016 | Transcriptome | |
31418903 | Evidence for the facultative intracellular behaviour of the fish pathogen Vibrio ordalii. | Avendano-Herrera R, Arias-Munoz E, Rojas V, Toranzo AE, Poblete-Morales M, Cordova C, Irgang R | J Fish Dis | 10.1111/jfd.13072 | 2019 | Animals, Cell Line, Fish Diseases/*microbiology, Flow Cytometry/veterinary, Fluorescent Antibody Technique, Indirect/veterinary, Microscopy, Confocal/veterinary, *Salmon, Vibrio/*physiology, Vibrio Infections/microbiology/*veterinary | ||
Metabolism | 32293041 | Identification and characterization of outer membrane vesicles from the fish pathogen Vibrio ordalii. | Echeverria-Bugueno M, Espinosa-Lemunao R, Irgang R, Avendano-Herrera R | J Fish Dis | 10.1111/jfd.13159 | 2020 | Animals, Bacterial Outer Membrane/*metabolism, Extracellular Vesicles/*metabolism, Fish Diseases/*microbiology, *Salmo salar, Vibrio/*pathogenicity/*physiology, Vibrio Infections/microbiology/*veterinary, Virulence |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8213 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19621) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19621 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
41338 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14976 | ||||
54249 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 38425) | https://www.ccug.se/strain?id=38425 | |||
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) | |||
68368 | Automatically annotated from API 20E | |||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
86327 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID7461.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121431 | Curators of the CIP | Collection of Institut Pasteur (CIP 103205) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103205 |