The mammalian alimentary tract harbors hundreds of species of commensal microorganisms that intimately interact with the host immune system. Within the gut, the immune system actively reacts with potentially pathogenic microbes, while simultaneously remaining ignorant towards the vast majority of non-pathogenic microbiota. The disruption of this delicate balance results in inflammatory bowel diseases. In this review, we describe the recent advances in our understanding of how host-microbiota interactions shape the immune system and how they affect the responses against pathogenic bacteria.