To understand the biological underpinnings of a complex system like our gut microbiota, we need tools that can perturb it. Currently, many studies on how the microbiome impacts our health are associative and descriptive: they lack mechanistic insight into microbe-microbe and microbe-host interactions. One reason for this is that gut bacterial species are not easy to culture in the lab, making the development of gene editing tools for them extremely challenging. However, deleting specific genes from specific strains in the gut microbiota could help assign function to them, and in turn determine how such functions influence our health. Several groups have recently developed promising gene editing tools for individual species of gut bacteria or entire bacterial communities. These tools could not only help the gut microbiome field advance from association to causation, but could form the basis of future therapeutics.