Comparative analysis of the gut microbiota of the wild nile tilapia (Oreochromis niloticus) across the seven reservoirs in Sri Lanka

Abstract

Nile tilapia (Oreochromis niloticus) is a commercially important freshwater fish species worldwide. The present study aims to compare the gut microbial communities of Nile tilapia O. niloticus across seven reservoirs in Sri Lanka, identify the core microbiota, and examine the environmental influences on microbial composition. Notably, the gut microbiota of O. niloticus varied significantly (p ≤ 0.05) by gender and exhibited a distinct composition across the seven reservoirs namely, Padaviya, Yanoya, Minneriya, Kaudulla, Rathkinda, Ulhitiya, and Udawalawe. The dominant bacterial genera included Cyanobium, Clostridium sensu stricto 1, Cetobacterium, and LD29. The richness and diversity of the intestinal microbiota were higher in the Rathkinda and Padaviya reservoirs. Genus Paracoccus and Roseomonas exhibited negative correlations with most other genera, while Romboutsia and Bacillus showed positive correlations with almost all other genera. A series of probiotic bacteria, including Bacillus and Exiguobacterium species, were isolated and are crucial for aquaculture. Some opportunistic pathogenic bacteria such as Plesiomonas, Aeromonas, Rothia and Staphylococcus were isolated from the gut of O. niloticus. The toxin-producing Cyanobium exhibited significant (p ≤ 0.05) negative correlations with multiple water quality parameters including chloride, total hardness, calcium, total alkalinity and total dissolved solids in the studied reservoirs. Our results could provide valuable insights into the assembly of gut microbiomes and sustainable development of the O. niloticus industry in various geographical locations.