The understanding of the human immune system and its responses to perturbations remains a considerable challenge to immunologists, in large part due to the diverse genetic makeup and environmental influence of individuals. Intersecting with these two factors is the enormous and diverse communities of microbes that colonize various parts of the body. These microbes, described as our microbiota, coevolve with us and coexist with our immune system, eliciting a mutualistic response. In advancing our immunological insights into diseases, it has become clear that we also need to identify the mechanisms that allow specific members of the microbiota to modulate the host’s immune health. From these studies, new connections between the microbiota and the immune system are starting to emerge. Disease states are often associated with changes in the composition and behavior of the microbiota, and this line of investigation will unveil therapeutic potential to treat infections, inflammatory diseases, and cancer.