Strain identifier

BacDive ID: 24660

Type strain: Yes

Species: Vibrio toranzoniae

Strain Designation: Vb 10.8

Strain history: <- CECT <- J. L. Romalde, University of Santiago de Compostela, Spain <- S. Balboa

NCBI tax ID(s): 1194427 (species)

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General

@ref: 21066

BacDive-ID: 24660

DSM-Number: 28519

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Vibrio toranzoniae Vb 10.8 is a mesophilic bacterium that was isolated from cultured Manila clam Ruditapes philippinarum.

NCBI tax id

  • NCBI tax id: 1194427
  • Matching level: species

strain history

  • @ref: 21066
  • history: <- CECT <- J. L. Romalde, University of Santiago de Compostela, Spain <- S. Balboa

doi: 10.13145/bacdive24660.20230509.8.1

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 toranzoniae
  • full scientific name: Vibrio toranzoniae Lasa et al. 2013

@ref: 21066

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio toranzoniae

full scientific name: Vibrio toranzoniae Lasa et al. 2013

strain designation: Vb 10.8

type strain: yes

Morphology

multimedia

  • @ref: 21066
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28519.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 21066
  • 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: 21066
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
21066--------+++++---+--++

Isolation, sampling and environmental information

isolation

  • @ref: 21066
  • sample type: cultured Manila clam Ruditapes philippinarum
  • host species: Ruditapes philippinarum
  • geographic location: Ría de Vigo
  • country: Spain
  • origin.country: ESP
  • continent: Europe
  • latitude: 42.3472
  • longitude: -8.6367

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Host#Invertebrates (Other)#Mollusca

Safety information

risk assessment

  • @ref: 21066
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21066
  • description: Vibrio toranzoniae partial 16S rRNA gene, type strain Vb 10.8T
  • accession: HE978310
  • length: 1507
  • database: ena
  • NCBI tax ID: 1194427

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio toranzoniae CECT 7225GCA_900089765contigncbi1194427
66792Vibrio toranzoniae strain CECT 72251194427.5wgspatric1194427
66792Vibrio toranzoniae strain Vb 10.81194427.3wgspatric1194427
66792Vibrio toranzoniae CECT 7225GCA_024347655completencbi1194427
66792Vibrio toranzoniae Vb 10.8GCA_001541335contigncbi1194427

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes93.006no
gram-positiveno98.731no
anaerobicno97.212no
aerobicyes86.073no
halophileyes68.39no
spore-formingno95.698no
motileyes91.797no
glucose-fermentyes85.324yes
thermophileno99.659no
glucose-utilyes87.959no

External links

@ref: 21066

culture collection no.: DSM 28519, CAIM 1869, CECT 7225

straininfo link

  • @ref: 88499
  • straininfo: 376927

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23280322Vibrio toranzoniae sp. nov., a new member of the Splendidus clade in the genus Vibrio.Lasa A, Dieguez AL, Romalde JLSyst Appl Microbiol10.1016/j.syapm.2012.11.0052012Aerobiosis, Anaerobiosis, Animals, Aquatic Organisms/microbiology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Bivalvia/microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Vibrio/*classification/genetics/*isolation & purification/physiologyGenetics
Genetics27034502Draft Genome Sequence of Vibrio toranzoniae Strain CECT 7225T.Lasa A, Gibas CJ, Romalde JLGenome Announc10.1128/genomeA.00212-162016
28194141Comparative Genomic Analysis of Two Vibrio toranzoniae Strains with Different Virulence Capacity Reveals Clues on Its Pathogenicity for Fish.Lasa A, Gibas CJ, Romalde JLFront Microbiol10.3389/fmicb.2017.000862017

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
21066Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28519Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28519)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
88499Reimer, 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 identifiers10.60712/SI-ID376927.1