Metagenomic analysis of gut microbiome from tilapia species across several regions in Japan

Tilapia is one of the most widely cultured fish species in the world. The host-associated microbiota plays essential roles in growth, metabolism, immunological responses, and adaptation. We used the 16S rRNA Illumina MiSeq sequencing to investigate the microbial composition, structure, and functions of tilapia species gut microbiota from five distinct regions in Japan. Our findings showed that the gut microbial community in fish was more strongly shaped by habitat water source than by tilapia species. The bacterial community of fish differs significantly from groundwater to river water. The beta diversity analysis indicated a strong separation of samples based on their water source. The fish gut microbiota was dominated by Fusobacteriota (25%), Proteobacteria (22%), Firmicutes (14%), and Cyanobacteria (12%) across all samples. Contrarily, the relative abundance of Cyanobacteria was higher in the groundwater group than in the river group, with a shift in the functional features of the community. Cetobacterium and Romboutsia were the most prevalent genera across all samples. This study sheds light on the gut microbiota of tilapia species in Japan. It contributes to our understanding of tilapia adaptability, which may aid in developing future tilapia aquaculture strategies in Japan. •The gut microbiome of the tilapia species differs based on their water source.•The predominance of Cyanobacteria in groundwater and Fusobacteriota in river samples.•Eight differential functional pathways were identified.•Salinity and conductivity may influence the gut microbial composition.