The Lung Microbiome: New Principles for Respiratory Bacteriology in Health and Disease

The principles of respiratory microbiology are being re-evaluated and re-written, starting with the debunked myth of lung sterility. The “terrain” of the respiratory ecosystem differs—anatomically and physiologically—from that of other mucosal sites, and changes dramatically in illness, when the dynamic homeostasis between host and microbiome is disrupted. Researchers are only just beginning to understand the contribution of viruses, phages, and fungi to the lung microbiome; thus, we have restricted our discussion to the bacterial microbiota of the lungs.