The principal goal of this research was to provide a detailed characterisation of the oyster microbiome and identify links between specific features of the microbiome and oyster disease and mortality events. The conceptual framework for this work is based upon: (i) increasing evidence, across a broad range of species, that the nature of a host organism’s microbiome exerts a fundamental control on host physiology and health, and (ii) the critical paucity in knowledge on the factors contributing to oyster health and the triggers for oyster mortality events and disease outbreaks. The research reported here involved a collaboration between the University of Technology Sydney (UTS) and the NSW Department of Primary Industries (DPI), whereby the UTS members of the team provided expertise in molecular microbial ecology and the DPI team members provided expertise and support in oyster physiology and ecology and aquaculture. The research involved a large-scale screening of the microbiomes of both Pacific Oysters and Sydney Rock Oysters using high-throughput DNA sequencing technologies, providing a characterisation of the microbial communities associated with oysters. The outcomes of this analysis revealed that for both Pacific Oysters and Sydney Rock Oysters, the oyster microbiome is remarkably variable among different oyster families, and over space and time, indicating that both intrinsic physiological features of the oyster host and environmental factors play a role in governing the oyster microbiome. Notably, despite this heterogeneity, a small sub-set of the microbiome was shown to be conserved across oysters within a species, pointing to the existence of a core group of microbes with intrinsic links to oyster ecology and condition. Similarly, a small group of microbes, including members of the Vibrio genus, were consistently associated with diseased or susceptible oysters, indicating a potentially antagonistic role of these microbes. These observations support the hypothesis that the oyster microbiome plays a role in defining oyster health, but also reveal substantial complexities related to the marked heterogeneity of the oyster microbiome over space and time. Appropriately considering this microbiome heterogeneity, while also sharpening focus on the few core microbiome members identified in this research, will be important requisites for
future efforts hoping to employ the oyster microbiome for diagnostic purposes.