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Dynamics of the Pacific oyster pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next-generation sequencing strategy.

  • Lasa, Aide1, 2
  • di Cesare, Andrea3
  • Tassistro, Giovanni1
  • Borello, Alessio1
  • Gualdi, Stefano4
  • Furones, Dolors5
  • Carrasco, Noelia5
  • Cheslett, Deborah6
  • Brechon, Amanda6
  • Paillard, Christine7
  • Bidault, Adeline7
  • Pernet, Fabrice8
  • Canesi, Laura1
  • Edomi, Paolo9
  • Pallavicini, Alberto9
  • Pruzzo, Carla1
  • Vezzulli, Luigi1
  • 1 Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy. , (Italy)
  • 2 Department of Microbiology and Parasitology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain. , (Spain)
  • 3 National Research Council-Water Research Institute (CNR-IRSA), Largo Tonolli 50, 28822, Verbania, Italy. , (Italy)
  • 4 Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland. , (Switzerland)
  • 5 IRTA, Sant Carles e la Ràpita, Tarragona, Spain. , (Spain)
  • 6 Fish Health Unit, The Marine Institute, Rinville Oranmore, Galway, Ireland. , (Ireland)
  • 7 Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la M, Université de Bretagne Occidentale - UMR6539 CNRS/UBO/IRD/Ifremer, Plouzané, France. , (France)
  • 8 Ifremer, Physiologie Fonctionnelle des Organismes Marins, UMR 6539 LEMAR (CNRS/Ifremer/IRD/UBO) Technopole Iroise, CS 10070, 29280, Plouzane, France. , (France)
  • 9 Department of Life Sciences, University of Trieste, Trieste, Italy. , (Italy)
Published Article
Environmental Microbiology
Wiley (Blackwell Publishing)
Publication Date
Dec 01, 2019
DOI: 10.1111/1462-2920.14750
PMID: 31325353


Infectious agents such as the bacteria Vibrio aestuarianus or Ostreid herpesvirus 1 have been repeatedly associated with dramatic disease outbreaks of Crassostrea gigas beds in Europe. Beside roles played by these pathogens, microbial infections in C. gigas may derive from the contribution of a larger number of microorganisms than previously thought, according to an emerging view supporting the polymicrobial nature of bivalve diseases. In this study, the microbial communities associated with a large number of C. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real-time PCR and 16SrRNA gene-based microbial profiling. A new target enrichment next-generation sequencing protocol for selective capturing of 884 phylogenetic and virulence markers of the potential microbial pathogenic community in oyster tissue was developed allowing high taxonomic resolution analysis of the bivalve pathobiota. Comparative analysis of contrasting C. gigas samples conducted using these methods revealed that oyster experiencing mortality outbreaks displayed signs of microbiota disruption associated with the presence of previously undetected potential pathogenic microbial species mostly belonging to genus Vibrio and Arcobacter. The role of these species and their consortia should be targeted by future studies aiming to shed light on mechanisms underlying polymicrobial infections in C. gigas. © 2019 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

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