Metagenomic analysis of gut microbiome in Nile tilapia, Oreochromis niloticus: Insights from cultured and lake populations

The application of high-throughput sequencing to investigate the gut microbiome has become increasingly frequent in aquaculture due to its role in monitoring the fish immune system and nutrient absorption. This study examines the gut microbiome of Nile tilapia ( Oreochromis niloticus ) from two distinct environments: a cultured pond and a natural lake. Using 16S rRNA Next-Generation Sequencing (NGS), the microbial communities within the gastrointestinal tract were characterized, and the impact of habitat on microbial diversity and composition was assessed. This study represents the first NGS-based study of the Nile tilapia microbiome in Malaysia. The findings showed that the lake population had significantly higher microbial diversity than the cultured pond population, likely attributable to the more diverse and natural diet in the lake. The dominant bacterial phyla differed by habitat, with Fusobacteriota (41.4 %) prevailing in lake samples and Firmicutes (71.1 %) in pond samples. Principal Coordinate Analysis (PCoA) revealed significant differences in gut microbiota between habitats. Despite these differences in microbial composition, most phyla were shared across both populations. Overall, these findings provide valuable insights into the gut microbiome of tilapia reared under Malaysian conditions, offering data to support the optimization of tilapia feed and management practices.