The human gut is home to trillions of microbes. The vast majority of the bacteria that inhabit the gut promote host health by aiding digestion and preventing pathogen colonization. How the host tolerates these beneficial commensals isn’t fully understood, but adaptive immune responses against commensals are characteristic of chronic inflammatory diseases. The Clasen lab studies the relationship between the host and its commensal microbiota to address this fundamental question. They focus on flagellated bacteria since flagellin is produced by both commensals and pathogens and is a target of the host innate immune system. The lab investigates the differential response to flagellins from pathogens and commensals using molecular and transcriptomic approaches in both organoid and mouse models, cell-mediated adaptive immune responses to commensal flagellins, and the development of antibody responses to commensal flagellins in disease states. These projects lay the groundwork for future studies into how the immune system responds to commensal microbiota broadly throughout host development.