This book comprehensively covers the microbiome in respiratory disease, from the initial research study to the disease-specific implications and related applications. Research on the respiratory microbiome is increasing in volume and scope. This reflects rapidly growing interest in the study of respiratory disease to understand how microbiota shape mechanisms of disease pathogenesis.  The respiratory tract spans the nasal passages, sinus cavities, oropharynx, and the tracheobronchial tree of the lungs.  In these compartments of the upper and lower respiratory tract, the microbiota have now been studied in the context of several chronic respiratory conditions. These include chronic sinusitis, allergic rhinitis, asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and pulmonary fibrosis, to name a few. The potential impact of ecological interactions (i.e., between microbes and between microbiota and host) within and across respiratory compartments is increasingly recognized.