Current research has shown that different sites of the human body house different bacterial communities. There is a strong correlation between an individual's microbial community profile at a given site and the onset of disease. Chronic Obstructive Pulmonary Disease (COPD) is a progressive lung disease resulting in narrowing of the airways and restricted airflow. Despite being the third leading cause of death in the United States, little is known about the differences in the lung microbial community profiles of healthy individuals vs. COPD patients. Metagenomics is the culture-independent study of genetic material obtained directly from samples. A metagenomic analysis of 56 individuals was conducted. Bronchoalveolar lavage (BAL) samples were collected from COPD patients, active or ex-smokers, and never smokers. 454 pyrosequencing of 16S rRNA was performed and analyzed using a newly designed, modular bioinformatic workflow. Substantial colonization of the lungs was found in all subjects and differentially abundant genera in each group were identified (including Tropheryma in COPD and Sneathia in smokers). These discoveries are promising and may further our understanding of how the structure of the lung microbiome is modified as COPD progresses. It is also anticipated that the results will eventually lead to improved treatments for COPD.