The lung harbours a diverse array of microbes whose dynamic composition is influenced by both host and environmental factors. Thus far, most studies have described the microbial composition of healthy or diseased lungs and provided an overview of the differences between topographical locations within the respiratory tract. However, insight into the functional mechanisms underlying host-microbe interactions and how they might drive lung health and disease are limited. This review provides an overview of the current mechanistic understanding of the microbiome, crosstalk between tissue compartments, and its involvement in respiratory diseases.