The respiratory microbiome is topographically distinct from that of the intestinal tract. Mounting evidence implicates microbial communities from both systems as likely modifiers of disease phenotype in asthma and COPD: the two most globally prevalent, yet heterogeneous, airway diseases. Over the past decade the Huang lab has co-led several clinical translational studies that have aimed to understand the links between airway and gut microbiota, and biological and clinical features of these diseases. This talk will highlight findings elucidated from both multi-center (NIH research networks) and single center study cohorts (Univ. of Michigan), including microbiota associations with immune response patterns, clinical markers of disease severity and emerging evidence of the effects of prescribed treatments.