![]() It is now recognized that host‐associated microbial communities (also named the microbiota) (Lederberg and McCray, 2001) are playing an important role in animal health by providing prominent services ranging from nutrient processing to protection from diseases. Recent advances in DNA sequencing technology is enabling new quantitative insights into the microbial community diversity associated with human and animal tissues (Yatsunenko et al., 2012 Yarza et al., 2014). 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 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. 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. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real‐time PCR and 16SrRNA gene‐based microbial profiling. In this study, the microbial communities associated with a large number of 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. Beside roles played by these pathogens, microbial infections in C. 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.
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