Strain identifier

BacDive ID: 17327

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
28174species
990998strain

strain history

@refhistory
8213<- CCUG <- CECT <- NCIMB <- M. H. Schiewe; DF3K <- E. J. Ordal
121431CIP <- 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

@refmotilityconfidencegram staincell shape
69480yes97.657
6948099.996negative
121431yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8213MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514f.pdf
41338Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121431CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8213positivegrowth28mesophilic
41338positivegrowth25mesophilic
54249positivegrowth26-30mesophilic
121431positivegrowth22-30
121431nogrowth37mesophilic
121431nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 54249
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836927897tryptophan-energy source
6836917632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin+fermentation
6836828053melibiose-fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12143117632nitrate-reduction
12143116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
121431oxidase+
121431alcohol dehydrogenase-1.1.1.1
121431catalase+1.11.1.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121431-+++-+----++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
8213----------------+-+-+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8213--+----++--+--------+
8213-----+---------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121431++-----+-++------------------------------------------------+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8213kidney of moribund coho salmon (Oncorhyncus kisutch)Oncorhyncus kisutchWashington, Purget SoundUSAUSANorth America
54249Kidney of moribund coho salmon,Oncorhyncus kisutchWashington,Purget SoundUSAUSANorth America
121431Animal, Moribund coho salmon, kidney tissueWashingtonUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#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

@refpathogenicity animalbiosafety levelbiosafety level comment
8213yes1Risk group (German classification)
1214312Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio ordalii DNA, 16S-23S rRNA intergenic spacer, partial sequence, strain: ATCC 33509AB255727260ena990998
20218Vibrio ordalii 16S rRNAD11214219ena28174
20218Vibrio ordalii 16S rRNAD11263214ena28174
20218Vibrio ordalii 16S rRNAD11312192ena28174
20218Vibrio 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 sequenceEU570972598ena990998
20218Vibrio 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 sequenceEU570973476ena990998
20218Vibrio ordalii strain ATCC 33509 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu, tRNA-Lys, and tRNA-Val genes, complete sequenceFJ666335724ena990998
20218Vibrio ordalii strain ATCC 33509 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu, tRNA-Lys, tRNA-Ala, and tRNA-Val genes, complete sequenceFJ666336821ena990998
8213V.ordalii gamma subclass (ATCC 33509) gene for 16S rRNAX706411480ena990998
8213V.ordalii (ATCC 33509T) gene for 16S ribosomal RNAX747181425ena990998

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio ordalii ATCC 33509990998.3wgspatric990998
66792Vibrio ordalii Schiewe DF3K, ATCC 335092513237346draftimg990998

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.586no
flagellatedyes85.728no
gram-positiveno99no
anaerobicno94.248yes
halophileno50no
spore-formingno95.677no
thermophileno98.703no
glucose-utilyes89.27no
aerobicyes78.416no
glucose-fermentyes80.487yes

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18429439Antigenic 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 RDis Aquat Organ10.3354/dao018722008Animals, 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/*veterinaryEnzymology
25667332Cell-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 RDis Aquat Organ10.3354/dao028202015Animals, 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
Genetics27382430The 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 RStand Genomic Sci10.1186/s40793-016-0166-62016Transcriptome
31418903Evidence 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 RJ Fish Dis10.1111/jfd.130722019Animals, Cell Line, Fish Diseases/*microbiology, Flow Cytometry/veterinary, Fluorescent Antibody Technique, Indirect/veterinary, Microscopy, Confocal/veterinary, *Salmon, Vibrio/*physiology, Vibrio Infections/microbiology/*veterinary
Metabolism32293041Identification and characterization of outer membrane vesicles from the fish pathogen Vibrio ordalii.Echeverria-Bugueno M, Espinosa-Lemunao R, Irgang R, Avendano-Herrera RJ Fish Dis10.1111/jfd.131592020Animals, Bacterial Outer Membrane/*metabolism, Extracellular Vesicles/*metabolism, Fish Diseases/*microbiology, *Salmo salar, Vibrio/*pathogenicity/*physiology, Vibrio Infections/microbiology/*veterinary, Virulence

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8213Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19621)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19621
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41338Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14976
54249Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38425)https://www.ccug.se/strain?id=38425
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86327Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7461.1StrainInfo: A central database for resolving microbial strain identifiers
121431Curators of the CIPCollection of Institut Pasteur (CIP 103205)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103205