Studies on marine epizootics are often based on the identification of a single pathogen. However, the one-pathogen-one-disease paradigm is not always sufficient to explain the disease, especially since the evidences on the role of microbiota in health and disease. Vibrio splendidus strains have been associated with Mytilus edulis mortality in France. To assess the role of mussel microbiota in the infectious process, we performed experiments combining the investigation of total microflora dynamics during a realistic experimental infection by V. splendidus and the monitoring of mussel survival and the dominance of potential opportunistic bacteria after antibiotic treatment. We found that Vibrio exposure affected the structure and predictive function of the mussel microbiota. Dysbiosis was accompanied with the appearance of a pathobiont dominated by Bacteroidetes and Fusobacteria phyla. The injection of a homogenate of infected organisms increased Mytilus mortality compared to the direct injection of Vibrio while the antibiotic pretreatment reduced the effect of pathogen exposure and mortalities. The decrease of opportunistic bacteria abundance in antibiotic pretreated animals confirmed their implication in pathogenesis. Our findings suggest that mussel disease results from a collaboration between external pathogens and pathobiont bacteria. Therefore, an insight into microbiota functions is needed to a better understanding of pathosystems.