The flexible portion of a bacterium’s genome—DNA that is exchanged with other bacteria through the process of horizontal gene transfer—allows it to rapidly adapt to changing environmental conditions by incorporating novel functions. These auxiliary genes can include those that confer resistance to antibiotics, enzymes involved carbohydrate degradation, mercury-resistance or virulence genes, and catabolic genes useful in bioremediation. Despite the importance of flexible DNA in shaping the roles of individual bacteria, basic facts about the frequency and conditions that promote gene exchange in natural ecosystems remain unknown. We aim to develop novel experimental and in silico methods to detect horizontal gene transfer occurring within natural microbial communities, starting with the gut microbiome, where rates of gene transfer likely exceed other microbial ecosystems. Our lab’s methods will shed light on the factors that influence microbial evolution in real-time.