Respiratory tract diseases represent some of the most common causes of mortality worldwide, yet the role of the respiratory tract’s resident microbiome is still underexplored in many of these diseases. In the present study, we examined the role of the respiratory microbiome in two diseases, COVID-19 and Chronic Lung Allograft Disfunction, as well as one related environmental exposure, the reuse of facemasks during the COVID-19 pandemic. In our COVID-19 cohort, we found that more severe disease was correlated with a loss of oropharyngeal microbiome diversity, and a reduction in the genera Haemophilus and Neisseria. Examining other COVID-19 cohorts from published literature found that this was a consistent signature, suggesting a possible indicator of severe disease that is consistent across patients. In our mask reuse study, we looked for changes in the respiratory tract microbiome associated with the reuse of disposable facemasks during the COVID-19 pandemic. We recruited two cohorts of participants, one group wearing a new facemask each day, another wearing one mask for a whole week. We found that while the bacterial burden on facemasks increased substantially with repeated use, this was not associated with any changes in the respiratory tract microbiome. Finally, in our CLAD cohort, we identified factors associated with lung function decline in lung transplant recipients. We collected microbiome samples during the first year post-transplant, and tracked lung function over the next eight years. We found three factors that correlated strongly with time to CLAD onset; expression of the cytokine IP10/CXCL10 immediately post-transplant, total bacterial burden at six weeks post-transplant, and the Streptococcus to Prevotella ratio at six months post-transplant. This work indicates that long term survival following lung allograft is dependent on microbiome alterations that occur during the first months, weeks, and even hours post-transplant. Ultimately, these three cohort studies lay the foundation for mechanistic studies of the respiratory tract microbiome in both acute and chronic lung conditions.