Real-time and field-friendly diet and gut microbiome metabarcoding analyses of skipjack tuna (Katsuwonus pelamis) with Oxford Nanopore Technology
Increasing climate pressures and limited access to pelagic ecosystems hinder timely and comprehensive monitoring of marine biodiversity. Gut content and microbiome analyses of opportunistic predators offer a valuable insight into study ecosystem dynamics. Recent advances in sequencing technologies, particularly Oxford Nanopore Technology (ONT), present opportunities for rapid and field-friendly assessments. This study evaluates the feasibility of ONT MinION for diet and gut microbiome analyses, comparing its performance with Illumina MiSeq using both mock communities and real gut samples of skipjack tuna. Two library preparation methods, PCR-based and PCR-free, were also tested to mitigate amplification bias.