The microbiota plays a critical role for human health and disease. However, how the host and microbiota interact and how this contributes to development of disease is still largely unknown. Overall, the aim of our group is to identify and study the specific molecular mechanisms by which microbes, which includes how commensal bacteria modulate host immunity and how this in turn impacts disease. We are particularly interested in immune responses in the lung including the response to respiratory pathogens such as influenza virus as well as chronic diseases such as idiopathic pulmonary fibrosis and diabetes. Specifically, it is our goal to characterize the role of both the gut and lung-resident microbiota and their products in controlling the host immune system and how this contributes to airway inflammation in different disease settings. This includes factors that directly impact the microbiota such as nutrition and other environmental influences. To achieve our aims, we employ state of the art OMICS methods to describe the complexity of the microbiota and its products, and use advanced in vivo gnotobiotic mouse models as well as in vitro translational organoid systems to establish the mechanistic and functional role of specific microbes in regulating the human immune system.