Changes in the gut microbiota have been implicated in a variety of disease states. In order to fully investigate the role of the microbiome in these diseases, it is critical to systematically probe the role of each individual species of bacteria in a given consortium. Current methods of probing the microbiome are unable to specifically target strains of interest in these diseases. Bacteriophage are a promising avenue to specifically target  strain in a native community due to their narrow host range, antibacterial properties, and ability to lyse host microbes. Here, we propose using lysogenic phage, phage integrated into the host genome, to deliver engineered genetic payloads to hosts of interest in an established microbiome. Using Bacteroides as a proof-of-concept target, we identified 14 prophage present in Bacteroides caccae. We showed that two of these prophage are capable of transducing DNA to a naïve host by using luciferase and antibiotic markers integrated into the prophage genome. As a proof-of-concept payload, we designed an inducible genetic killswitch using an endogenous Bacteroides toxin. This system reduced a targeted bacterial population both in vitro and in vivo. The combination of the prophage with the killswitch could allow for targeted strain removal in an established microbial community in a mouse gut. Such a technique would allow for evaluation of specific bacterial strains on disease.