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The use of novel methods to study the microbiome has revolutionized our understanding of the microbial communities that reside on mucosal surfaces. While culture-based methods and Koch’s postulates produced advances in medicine that moved the field into the modern era through development of antimicrobials and an understanding of microbial pathogenesis, these methods are inherently biased and reductive in scope.

This chapter constitutes an introduction to the methods used in microbiome research. Highlighted are specific considerations for lung research, as well as what is known about the lung microbiome in health and selective disease states. Table 121-1 outlines terms used in this chapter and commonly employed in the microbiome literature. Since this is a rapidly evolving field, inevitably, we will witness advances in a variety of areas. Understanding microbiome composition in disease states, identifying predictive microbiome features, and establishing prognostic biomarkers, host–microbiome interactions, and, potentially, therapeutics that affect the microbiome or that are microbially derived, are reasonable goals. Given the dynamic nature of the field, our objective is to provide an overview of foundational principles, to highlight considerations for understanding the microbiome in the lung, and to suggest future directions in lung microbiome research.

TABLE 121-1Microbiome Terminology

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