Microbiome of wild oysters: assessing diversity and detecting potential pathogens using a metabarcoding approach

This study demonstrates the utility of metabarcoding for characterizing microbial communities and detecting pathogens in two oyster species, C. gigas and S. cucullate, across geographically distinct regions. Bacterial richness was influenced by environmental gradients such as sea surface temperature and latitude, while several key protist pathogens (P. marinus, B. ostreae, H. costale) were detected at low infection intensities in asymptomatic oysters. Limitations in protist detection due to sequencing depth and host amplification highlight the need for optimized primers and complementary approaches such as multiomics and microscopy. These findings provide a foundation for understanding host-microbe-environment interactions. Specifically, our results can inform targeted monitoring programs for the early detection of pathogens and guide selective breeding initiatives for disease-resistant oyster strains, thereby enhancing the long-term resilience of oyster aquaculture under changing environmental conditions.