Strain identifier

BacDive ID: 17351

Type strain: No

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)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 17983

BacDive-ID: 17351

DSM-Number: 25291

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, ovoid-shaped, animal pathogen

description: Vibrio owensii R-40496 is a mesophilic, Gram-negative, motile animal pathogen that was isolated from mucus of the endemic coral Mussismilia hispida.

NCBI tax id

NCBI tax idMatching level
1280004strain
696485species

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/bacdive17351.20230509.8.1

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 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
29735negative3 µm1 µmovoid-shapedyes
69480negative99.982
69480yes97.18

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17983VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115)yeshttps://mediadive.dsmz.de/medium/115Name: 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
17983BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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

@refgrowthtypetemperaturerange
17983positivegrowth28mesophilic
29735positivegrowth07-42
29735positiveoptimum26mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.634

halophily

  • @ref: 29735
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 3.75 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2973521217L-alaninamide+carbon source
2973516449alanine+carbon source
2973540585alpha-cyclodextrin+carbon source
2973522653asparagine+carbon source
2973535391aspartate+carbon source
2973517057cellobiose+carbon source
2973523652dextrin+carbon source
2973528757fructose+carbon source
2973524265gluconate+carbon source
2973517234glucose+carbon source
2973529987glutamate+carbon source
2973517754glycerol+carbon source
2973528087glycogen+carbon source
2973517596inosine+carbon source
2973524996lactate+carbon source
2973517306maltose+carbon source
2973529864mannitol+carbon source
2973537684mannose+carbon source
2973551850methyl pyruvate+carbon source
29735506227N-acetylglucosamine+carbon source
2973517992sucrose+carbon source
2973526986threonine+carbon source
2973517748thymidine+carbon source
2973527082trehalose+carbon source
2973553423tween 40+carbon source
2973553426tween 80+carbon source
2973516704uridine+carbon source
2973517632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan+energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29735acid phosphatase+3.1.3.2
29735alkaline phosphatase+3.1.3.1
29735alpha-galactosidase+3.2.1.22
29735catalase+1.11.1.6
29735gelatinase+
29735cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29735Vibrio sp. LMG 20370 partial 16S rRNA gene, strain LMG 20370AJ3450661470nuccore696485
17983Vibrio communis strain R-40496 16S ribosomal RNA gene, partial sequenceGU0786721470ena696485

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio owensii LMG 25430GCA_000400325scaffoldncbi1280004
66792Vibrio owensii LMG 254301280004.3wgspatric1280004
66792Vibrio owensii LMG 254302568526433draftimg1280004

GC content

@refGC-contentmethod
1798345.92sequence analysis
2973545.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.797yes
flagellatedyes89.21no
gram-positiveno98.538no
anaerobicno97.302no
aerobicyes85.289no
halophileyes53.153no
spore-formingno93.153no
thermophileno99.559yes
glucose-utilyes88.406no
glucose-fermentyes88.348yes

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

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17983Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25291)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25291
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
29735Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2611728776041
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)
68369Automatically annotated from API 20NE
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
86352Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362408.1StrainInfo: A central database for resolving microbial strain identifiers