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

The Pacific oyster (Crassostrea gigas) and the hooded oyster (Saccostrea cucullate) are ecologically and economically important species in the northwestern Pacific Ocean. However, sustainable oyster farming faces challenges from pathogenic diseases and environmental changes. Understanding microbial diversity in oysters is essential for managing pathogens, maintaining healthy microbial communities, and addressing microbial imbalances. This study aimed to investigate the diversity and composition of bacterial and protist communities in wild oysters from South Korea (C. gigas), Taiwan, and the Philippines (S. cucullata) using a metabarcoding approach.

Gill tissue and environmental DNA (eDNA) samples were analyzed to assess microbial community structure across species and regions. Bacterial richness significantly exceeded protist richness in all samples. Bacterial diversity was negatively correlated with sea surface temperature and positively correlated with latitude, indicating that temperature is a key driver of regional variation in bacterial community composition. Several potentially pathogenic protist and bacterial taxa were detected, including Perkinsus marinus, Bonamia ostreae, Haplosporidium costale, and Vibrio bathopelagicus. Notably, P. marinus and B. ostreae were identified in S. cucullata from Taiwan, while H. costale was detected in C. gigas from South Korea. Most pathogens occurred at low infection intensities and without clinical signs of disease. Challenges in detecting protist diversity due to sequencing depth and host-derived nontarget amplification were also noted, highlighting the importance of using protist-specific primers.

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.