Metagenomic analysis of the gut microbiome of Nile tilapia (Oreochromis niloticus) from biofloc andpond aquaculture systems in Kerala, South India

Nile tilapia (Oreochromis niloticus) is one of the most commonly cultured fish species in global aquaculture, with production expected to increase further due to its strong culture performance and resistance to various environmental conditions. The gut microbiota significantly affects the host’s health and the gut of Nile tilapia harbour a diverse microbial community. An experimental study was conducted to analyse the bacterial composition and functional profile of the gut microbiota of Nile tilapia from two different aquaculture systems, Biofloc and Pond culture systems in Kerala, South India. Bacterial communities in the gut of tilapia collected from two systems were classified down to the genus level using 16S rRNA amplicon sequencing. The most prevalent bacterial phyla in the Pond group were Firmicutes, Proteobacteria and Fusobacteria, while Bacteroidetes, Firmicutes and Proteobacteria dominated the biofloc group. At the genus level, Streptococcus and Pseudomonas were the most abundant in the Pond group, whereas Prevotella and Blattobacterium were more prevalent in the Biofloc group. Higher microbial diversity was observed in the gut microbiome of Nile tilapia from the biofloc group. The functional profile of the gut microbiome of Nile tilapia exhibited alterations between the two aquaculture systems. The functional profile of the gut microbiome of Nile tilapia assessed by PiCrust2 revealed that the membrane transport-associated function was predominant in the Pond group and carbohydrate metabolism-associated function in the Biofloc group. The study illustrated how the host environment significantly impacts the composition, diversity and functional profile of the gut microbiome of Nile tilapia. Keywords: Biofloc, Gut microbiota, Nile tilapia, Metagenomics