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Annu Rev Physiol. 2016;78:481-504. doi: 10.1146/annurev-physiol-021115-105238. Epub 2015 Nov 2.

The Microbiome and the Respiratory Tract.

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Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109; email:
Department of Internal Medicine, Weill Cornell Medical College, New York, NY 10065.
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109.


Although the notion that "the normal lung is free from bacteria" remains common in textbooks, it is virtually always stated without citation or argument. The lungs are constantly exposed to diverse communities of microbes from the oropharynx and other sources, and over the past decade, novel culture-independent techniques of microbial identification have revealed that the lungs, previously considered sterile in health, harbor diverse communities of microbes. In this review, we describe the topography and population dynamics of the respiratory tract, both in health and as altered by acute and chronic lung disease. We provide a survey of current techniques of sampling, sequencing, and analysis of respiratory microbiota and review technical challenges and controversies in the field. We review and synthesize what is known about lung microbiota in various diseases and identify key lessons learned across disease states.


16S rRNA; culture independent; lung; microbial ecology; microbiota; pulmonary

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