Low-level phage residues in manure are associated with shifts in microbial communities and resistance-related profiles.

Bacteriophages are increasingly being explored as alternatives to antibiotics in livestock production systems. However, the ecological impacts of residual phages excreted through feces after phage administration remain poorly understood. Here, we established a 42-day manure microcosm system to evaluate the ecological responses associated with fecal input containing residual phages from chickens orally administered a phage cocktail. Although the excreted phage fraction was relatively low (<1% of the administered dose; 4.28 ± 0.027 log10 PFU·day⁻1), it was associated with reduced bacterial diversity and decreased co-occurrence network complexity. These changes were accompanied by increased relative abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Notably, the relative enrichment of Psychrobacter was closely associated with resistance-related traits, suggesting that shifts in specific bacterial taxa may contribute to ARG and MGE dynamics. Collectively, our findings suggest that fecal input containing residual phages may have previously underappreciated ecological implications, particularly with respect to microbial community restructuring and resistance-related gene dynamics. These findings underscore the importance of continued investigation into the environmental dimensions of phage applications, contributing to their responsible development under a One Health framework.