Microbiome Diversity of the Gut of Clarias gariepinus Across Aquaculture and Wild Populations in Oyo State, South West Nigeria

This study characterises and compares the gut microbiome diversity of wild and aquaculture-reared Clarias gariepinus in Oyo State, South West Nigeria, addressing a significant gap in understanding how production environment shapes the gut microbial ecology of Nigeria's most important aquaculture fish species. Gut microbiome composition influences digestion efficiency, immune function, disease resistance, and meat quality, and management-specific differences may explain observed production performance variations. Gut contents from the midgut were collected from 30 wild fish from Asejire Reservoir and 30 each from three commercial catfish farms. Total DNA was extracted and the 16S rRNA gene V3-V4 region was amplified and sequenced using Illumina MiSeq. Amplicon sequence variants were analysed using QIIME2 and classified against SILVA reference databases. Alpha diversity, beta diversity, and differential abundance analysis were performed. Wild fish showed significantly higher gut microbiome alpha diversity than farm fish across all farms. Proteobacteria and Fusobacteria dominated in wild fish while Firmicutes and Proteobacteria dominated in farm fish. Cetobacterium, a producer of Vitamin B12, was significantly more abundant in wild fish gut communities. Farm-specific dietary composition was the strongest predictor of microbiome structure. The study provides the first gut microbiome characterisation for Nigerian Clarias gariepinus and identifies dietary manipulation as the primary lever for microbiome optimisation in commercial aquaculture to improve gut health and production efficiency. Keywords: gut microbiome, Clarias gariepinus, aquaculture, wild fish, 16S rRNA.