Dr. Morris’ research program has focused on understanding the epidemiology and mechanisms of HIV-associated lung diseases in the current era of antiretroviral therapy and in the role of the microbiome in lung disease. She has established multicenter cohorts investigating lung disease to perform clinical, translational, and basic studies. Discoveries from these cohorts include the bacterial and fungal communities in the lung microbiome, high prevalence of pulmonary function abnormalities in HIV-infected smokers and non-smokers, the independent contribution of HIV to pulmonary impairment, and linking lung function abnormalities to systemic and lung inflammation. Her group has also investigated the role of microbiome in chronic obstructive pulmonary disease in both HIV-infected and HIV-uninfected individuals. In particular, she determined that low levels of Pneumocystis in the lungs of both HIV-infected and non-HIV-infected individuals are associated with development and/or progression of COPD. Current studies include relationship of the microbiome of distant sites to lung disease, functional roles of the lung microbiome, and large, multi-center studies of lung function in HIV-infected and HIV-uninfected individuals.