ABSTRACT
The “microbiome” has been defined as “a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment, and especially the collection of microorganisms living in or on the human body.” 1 We are just beginning to understand how the microbiome interacts with the human host, and how this interaction contributes to health and disease. The microbiome has traditionally been investigated using culture-based methods. However, the advent of culture-free techniques to probe microbial sequences in recent years has vastly improved our ability to evaluate the microbiome. Much of the effort in humans has concentrated on the bacterial microbiome, the focus of this chapter. Yet, related to the advances in high-throughput technologies, viral and fungal communities are beginning to be analyzed as well. There is ever-increasing evidence that the microbial environment on human mucosal surfaces, specifically the airways and gastrointestinal tract, shape the development, maintenance, and heterogeneity of acute and chronic responses in airway disease.
