Gut Microbiome Dynamics in Farmed Tilapia: A Comparative Analysis of Fingerlings and Adults Infected with Tilapia Lake Virus

Abstract

Tilapia lake virus (TiLV) poses a significant threat to global tilapia aquaculture, yet its impact on the gut microbiota across developmental stages remains poorly understood. This study aimed to compare the gut microbial composition and functional potential of TiLV-infected adult and fingerling tilapia (Oreochromis niloticus) from aquaculture systems, using 16S rRNA gene sequencing and PICRUSt2-based prediction. Phylum-level analysis revealed that Proteobacteria dominated in adults, whereas fingerlings exhibited higher levels of Verrucomicrobiota, followed by Proteobacteria and Actinobacteriota. Genus-level differences were prominent: Acinetobacter, Novosphingobium, and Methylobacterium dominated in adult samples, while fingerlings showed an increased abundance of Akkermansia. Alpha diversity was slightly higher in adults, though not statistically significant. Beta diversity analysis revealed greater inter-individual variation among adults, while fingerlings exhibited tighter clustering, indicating a more conserved microbiota. Functional prediction showed enrichment of the membrane transport pathway in fingerlings. In contrast, adults showed higher activity in pathways related to replication and repair, nucleotide metabolism, metabolism of cofactors and vitamins, energy metabolism, and folding, sorting, and degradation. These findings demonstrate apparent life-stage-dependent differences in gut microbiota structure and function in TiLV-infected tilapia. Understanding these microbial patterns may inform age-specific strategies for disease management and microbiome modulation in aquaculture.