The human respiratory tract microbiome in health and disease

Recent studies have focused on defining the microbial populations living in association with the human body—referred to as the human microbiome. A common goal of microbiome research is to understand the type and range of normal microbial residents to establish a baseline for disease comparison. Through these studies, host-microbe relationships have been found to be important at many body sites and are connected with environmental influences. This dissertation focuses on the human respiratory tract, and explores two aspects of its microbiome: the normal structure of microbial populations colonizing the healthy host, and their disruption in respiratory disease. The upper airways are in open communication with both the external environment and the lung. Maintenance of healthy bacterial populations is important for reducing risk of both upper and lower tract disease. We first characterize the bacterial flora in the healthy upper airways by analyzing bacterial lineages from the naso- and oropharynx and assessing alterations with cigarette smoking. We found that the composition of upper airway microbiota is characteristically structured in health and systematically disordered by chronic exposure to cigarette smoke. We then define microbiota of the lower airways and assess its relationship to upper airway populations. We found that the healthy lung does not have a distinct microbiome, but instead contains low amounts of bacterial lineages indistinguishable from the upper airways. Through this study, we establish sampling methods for definitive analysis of lung microbiota using stringent bronchoscopy. Secondly, we characterize changes in respiratory flora in individuals with lung disease. We start by developing analytic methods to identify lung-enriched organisms for application with lung samples collected by routine clinical bronchoscopy. We then studied both bacteria and fungi from lung transplant recipients to define the impact of transplantation on lung infection and explore its relationship to graft failure. We show that markedly aberrant microbial communities and specific bacterial organisms, some not previously recognized, colonize the lung following transplant. We additionally develop tools to aid in the diagnosis of lung infections and add quantitative information to standard microbial culture techniques. Lastly, we use a metagenomic approach to detect covariation between bacteria and fungi within the respiratory tract of lung transplant subjects. We present data on the influences of specific fungi on the overall bacterial community and identify significant interactions between organisms. These results underline the central role of homeostatic microbial colonization to respiratory health, and the potential for utilizing deep sequencing data to illuminate microbial drivers of respiratory disease