Bacteriophages are the most abundant biological entities on Earth. They are known to be involved in the regulation of microbial ecology, diversity, and virulence. Their relationships with their bacterial hosts and their functional importance in the respiratory tract are however poorly understood in both health and disease. We characterized the viromes found in the bronchoalveolar lavages (BAL) of patients with lung disorders such as alpha-1 anti-trypsin deficiency and sarcoidosis. Our goal is to explore the taxonomy, diversity, and functionality of the identified phages to understand the role they play in structuring and influencing the lung microbiome. Additionally, bacterial 16S data will be integrated with this virome data to explore phage-host dynamics in the lung during disease. This work will increase our understanding of the ecological relationships between phages and their hosts in the human respiratory tract.