Strain identifier

BacDive ID: 132931

Type strain: Yes

Species: Vibrio metoecus

Strain Designation: OP3H

Strain history: CIP <- 2013, Y. Boucher, Alberta Univ., Edmonton, Canada: strain 0P3H "Vibrio metecus"

NCBI tax ID(s): 1481663 (species)

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General

@ref: 24719

BacDive-ID: 132931

DSM-Number: 104290

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

description: Vibrio metoecus OP3H is a mesophilic, motile bacterium that was isolated from water of oysterpond.

NCBI tax id

  • NCBI tax id: 1481663
  • Matching level: species

strain history

@refhistory
24719<- CIP <- P.C. Kirchberger et al.; OP3H
120925CIP <- 2013, Y. Boucher, Alberta Univ., Edmonton, Canada: strain 0P3H "Vibrio metecus"

doi: 10.13145/bacdive132931.20250331.9.3

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 metoecus
  • full scientific name: Vibrio metoecus Kirchberger et al. 2014

@ref: 24719

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio metoecus

full scientific name: Vibrio metoecus Kirchberger et al. 2014

strain designation: OP3H

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotilitycell shape
125439negative99.4
12543890.621yes
125438negative99.917
120925negativeyesrod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24719TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
120925CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 24719
  • growth: positive
  • type: growth
  • temperature: 28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 96.9

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.4

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
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368arginine dihydrolase-3.5.3.6
68368cytochrome oxidase-1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368lysine decarboxylase+4.1.1.18
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
24719+-+++---+-+++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
24719water of oysterpondMassachussettsUSAUSANorth America
120925Animal, Oyster pondFalmouth, MA, USA , MassachusettsUnited States of AmericaUSANorth America2006-10-02

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Environmental#Aquatic#Pond (small)

taxonmaps

  • @ref: 69479
  • File name: preview.99_25.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_20;97_21;98_24;99_25&stattab=map
  • Last taxonomy: Vibrio cholerae
  • 16S sequence: KJ647312
  • Sequence Identity:
  • Total samples: 13905
  • soil counts: 252
  • aquatic counts: 4727
  • animal counts: 8651
  • plant counts: 275

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
1209252Risk group (French classification)
247192Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24719
  • description: Vibrio metoecus strain OP3H 16S ribosomal RNA gene, partial sequence
  • accession: KJ647312
  • length: 1411
  • database: nuccore
  • NCBI tax ID: 1481663

Genome sequences

  • @ref: 66792
  • description: Vibrio metoecus OP3H
  • accession: GCA_000696385
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1481663

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.917no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.299no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no67.468no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.568no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes90.621no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.4
125439BacteriaNetmotilityAbility to perform movementyes84.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.9

External links

@ref: 24719

culture collection no.: DSM 104290, CIP 110643, LMG 27764

straininfo link

  • @ref: 91209
  • straininfo: 390544

literature

  • topic: Phylogeny
  • Pubmed-ID: 24972615
  • title: Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens.
  • authors: Kirchberger PC, Turnsek M, Hunt DE, Haley BJ, Colwell RR, Polz MF, Tarr CL, Boucher Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.060145-0
  • year: 2014
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Humans, Molecular Sequence Data, Multilocus Sequence Typing, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, United States, Vibrio/*classification/genetics/isolation & purification
  • topic2: Pathogenicity

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
24719Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104290Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104290)
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91209Reimer, 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-ID390544.1
120925Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110643Collection of Institut Pasteur (CIP 110643)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG