Our central hypothesis is that post-pneumonia changes in the lung microbiome are associated with declines in lung function and the development of COPD in HIV- infected persons. Aim 1: To compare the composition of the lung microbiome at baseline and 3-months and 1- year after acute pneumonia treatment using a standardized phylogenetic microarray (PhyloChip). Aim 2: To compare the structure of the lung microbiome at baseline and 3-months and 1-year after acute pneumonia treatment using high-throughput DNA sequencing (Illumina MiSeq). Aim 3: To correlate the lung microbiome composition and structure with changes in lung function and development of COPD in this cohort. To address these aims, we will conduct a longitudinal study of 25 HIV-infected Pneumocystis pneumonia (PCP) subjects and 25 HIV-infected TB subjects, and we will perform research bronchoscopy at 3-months and 1-year after the completion of pneumonia treatment. We will compare the lung microbiome in these individuals at the time of pneumonia to the lung microbiome after the completion of treatment using PhyloChip and MiSeq and will correlate microbiome composition and structure with lung function and chest computed tomography measurements. This proposal studies the convergence of four of the greatest causes of morbidity and mortality in the world. Worldwide, HIV/AIDS, pneumonia, TB, and COPD are among the top 10 causes of death. The proposed studies have the potential for advancing our knowledge of the link between HIV-associated pneumonias, including TB, and COPD.