Polymicrobial infection defines a combination of microorganisms, including viruses, bacteria, fungi, and sometimes parasites, which are simultaneously associated with an infected site. While the idea of polymicrobial infections is common nowadays, most clinical laboratories still focus on the culturing and identification of a single pathogen. The biological implications attributed to these singular microbial infections are deceptive, especially when considering the multiple complex interactions associated with polymicrobial infections. This dissertation used Cystic Fibrosis (CF) as a study system for polymicrobial infections in the lung. CF is a genetic disease caused by mutations in the Cystic Fibrosis Transmembrane Regulator (CFTR) gene. CF affects multiple organs across the body, but pulmonary infection remains the main cause of morbidity and mortality. Studying CF lungs is challenging. Here a set of comprehensive methods was developed to simultaneously study the viral, microbial, and host genetics using metagenomics and metatranscriptomics approaches. Many of the bacteria found in the lungs of CF patients are of oral origin. Detailed genetic analyses showed that these bacteria adapt to the CF lungs by acquiring essential genes while losing non-essential ones. One example is Rothia mucilaginosa _ an organism that is present in more than 80% of San Diego patients. De novo assembly of a near-complete R. mucilaginosa genome showed potential physiological adaptations through the acquisition of multiple genes. A survey of more than 20 CF patients in San Diego revealed that every patient harbors a unique microbial community, suggesting that CF patients require personalized medicine for the treatment of their lung infections. Despite these personalized differences in microbial taxonomical profiles across CF patients, the functional potential across these different microbial communities is highly similar. The conserved functional potential in CF microbes allows them to carry out aerobic and anaerobic respirations, as well as fermentation, highlighting the importance of anaerobes in the CF lungs. CF microbes regulate their metabolic activities in response to perturbations. In vitro community culturing of CF microbes showed that the anaerobes were sensitive to antibiotics commonly used in CF patients and their metabolic activities could be associated with the patient's health. The role and importance of CF anaerobes and their survival mechanisms are illustrated in this study. In summary, this dissertation provides novel insights into polymicrobial infections in CF lungs and demonstrates the potential and advantages of coupling omics and clinical approaches for the study of other complex polymicrobial infections.