Technical Abstract: Antibiotics are a cost-effective tool for improving feed-efficiency in agricultural animals, but the full scope of their collateral effects is not understood. Antibiotics have been shown to induce prophage-mediated gene transfer in certain bacterial strains; therefore, one collateral effect could be prophage induction in the gut microbiome at large. Here we used metagenomics to evaluate the effect of two in-feed antibiotics (carbadox and ASP250 [chlortetracycline, sulfamethazine, and penicillin]) on swine fecal phage metagenomes (viromes). We also monitored the bacterial community using 16S rRNA gene sequencing. ASP250, but not carbadox, caused significant population shifts in both the phage and bacterial communities. Antibiotic resistance genes, such as multidrug resistance efflux pumps, were identified in the viromes, but in-feed antibiotics caused no significant changes in their abundance. The abundance of integrase-encoding genes was significantly increased in the medicated versus non-medicated viromes, demonstrating the induction of prophages with antibiotic treatment. Phage-bacteria population dynamics were also examined. We observed a decrease in the abundance of Firmicutes bacteria (prey) when Firmicutes phages (predators) were abundant, supporting the “kill-the-winner” ecological model of population dynamics in the swine fecal microbiome. Our data show that gut ecosystem dynamics are influenced by phages, and that prophage induction is a collateral effect of in-feed antibiotics.