Heterogeneous bacterial communities in gills and intestine of Nile tilapia (Oreochromis niloticus) and in water and sediments of aquaculture ponds in Bangladesh

Tilapia aquaculture contributes significantly to the nutritional requirements of humans. Because microbes play a pivotal role in maintaining the host's physiology and biochemistry, research on the microbiomes associated with tilapia and in the rearing pond water and sediment can contribute to increased production. We applied 16S rRNA gene amplicon sequencing to elucidate the bacterial community structures in the gills and intestine of Nile tilapia as well as in the water and sediment of their rearing ponds. We identified a total of 9770 bacterial Operational Taxonomic Units (OTUs) in all the samples. The sediment samples, which generated 3884 unique OTUs, had the highest level of alpha-diversity (Shannon index, P < 0.01) among all the samples. Fusobacteria (59%) predominated and constituted the indicator phylum in tilapia gills, while Proteobacteria was prevailed in water (52%), sediment (28%), and intestine (33%). The bacterial community structures of the gills and intestine were not much similar to those of the surrounding water and sediment, probably due to host-specific microbial selection. More than 70% of the bacterial flora were beneficial, whereas nearly 10% were pathogenic in gills and intestine of tilapia. This study aims to explore the microbiome of tilapia aquaculture in Bangladesh, and the results suggest that the microbial communities in tilapia gills and intestine are in a eubiotic state, which indicates a healthy state for better growth and production of Nile tilapia aquaculture.