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The holobiont theory expands the notion of individual multicellular organisms as a community composed of a host and all its associated microorganisms. This concept has been extensively studied in the field of aquaculture, where increasing evidence has highlighted the importance of the host associated microorganisms in species fitness. Here, we focus our review on mollusc and crustacean species in which microbiota dysbiosis has recently been described in the context of various diseases, resulting in significant economic losses. Influencing the holobiont structure through the use of probiotics is a potential strategy that could improve the fitness or the robustness of cultivated species. We discuss here the possibility of developing microbiome targeted prophylactic approaches by promoting (1) methods to identify host microbial community that fosters good health status and (2) early life microbial education to favour long-term resistance to stress or disease. This review aims to inform the aquaculture industry about potential strategies in rearing practices to mitigate diseases and economic losses.

The Pacific cupped oyster Crassostrea gigas is one of the most “globalized” marine invertebrates and its production is predominant in many parts of the world including Europe. However, it is threatened by mortality events associated with pathogenic microorganisms such as the virus OsHV-1 and the bacteria Vibrio aestuarianus. C. gigas is also a host for protozoan parasites including haplosporidians. In contrast with Haplosporidium nelsoni previously detected in Europe, H. costale was considered exotic although its presence in French oysters was suggested in the 1980s based on ultrastructural examination. Here, a combination of light and transmission electron microscopy, PCR and sequencing allowed characterizing the presence of the parasite in the context of low mortality events which occurred in 2019 in France. Histological observation revealed the presence of uninucleated, plasmodial and spore stages within the connective tissues of some oysters. Ultrastructural features were similar to H. costale ones in particular the presence of axe-shaped haplosporosomes in spore cytoplasms. Three fragments of the genome including partial small subunit rRNA gene, the ITS-1, 5.8S and ITS-2 array and part of the actin gene were successfully sequenced and grouped with H. costale homologous sequences. This is the first time that the presence of H. costale was confirmed in C. gigas in France. Furthermore, a TaqMan real-time PCR assay was developed and validated (DSe = 92.6% (78.2-99.8) and DSp = 95.5% (92.3-98.6)) to enable the rapid and specific detection of the parasite. The application of the PCR assay on archived samples revealed that the parasite has been present in French oyster populations at least since 2008. Considering the little information available on this parasite, the newly developed TaqMan assay will be very helpful to investigate the temporal and geographic distribution and the life cycle of the parasite in France and more generally in C. gigas geographic range.

Although vibrios are frequently associated with marine organisms mortality outbreaks, knowledge on their ecology and pathogenicity is sparse, thus limiting disease management and prophylactic strategies. Here, we investigated V. aestuarianus infection onset and progression in the wild, taking advantage of a “claire” pond: a semi‐closed system with limited seawater renewal, theoretically more adapted to disease transmission. We showed a positive association of the bacteria with oysters, which can constitute a reservoir for the bacteria in the winter. Moreover, passage through oysters was found to be necessary for experimental disease reproduction as vibrios shedding from diseased oysters has higher infectivity than from in vitro grown. We next developed an experimental “ecologically realistic” infection model in a mesocosm, allowing infection by natural route. By means of this non‐invasive protocol, we analysed the pathogenesis of the bacteria and demonstrated the importance of haemolymph for initial colonisation and the septicaemic nature of this disease.