Comparative analysis of gut virome signatures between ducks raised in aquatic and dryland environments

This study comprehensively compared the viral community structure, functional potential, and virulence factors in ducks reared under WOW (without water) and WW (with water) conditions. Alpha diversity analysis indicated that the WW group exhibited significantly higher Shannon and Simpson indices compared with the WOW group (P < 0.01), though viral richness did not differ significantly between groups (P > 0.05). Beta diversity analyses (PCoA, and NMDS) revealed distinct separations between the viral communities of the two groups, highlighting the impact of rearing systems on viral composition. LEfSe analysis identified 35 viral families as biomarkers, with Crevaviridae, Drexlerviridae, and Demerecviridae enriched in the WOW group, while Straboviridae, Herelleviridae, and Mimiviridae were predominant in the WW group. Taxonomic composition analysis demonstrated that the WW group had significantly reduced abundances of Uroviricota and Spinunavirus but increased abundances of Nucleocytoviricota and Eurybiavirus (P < 0.05). Functional annotation revealed that viral genes in the WW group were enriched in core viral processes (e.g., virion assembly, DNA replication) and metabolic pathways (e.g., nucleotide metabolism, carbohydrate metabolism). Additionally, the WW group showed altered profiles of CAZymes and virulence factors, with increased antimicrobial resistance and biofilm formation capabilities. These findings demonstrate that water exposure reshapes the duck gut virome by enhancing viral diversity, altering taxonomic structure, and activating functional pathways associated with pathogenicity and nutrient metabolism. This study provides critical insights into the ecological impact of rearing systems on viral communities and offers a foundation for optimizing duck farming practices to mitigate health risks.