The Microbiome and the Respiratory Tract Review uri icon


MeSH Major

  • Lung Diseases
  • Microbiota
  • Respiratory System


  • 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.

publication date

  • February 10, 2016



  • Review



  • eng

PubMed Central ID

  • PMC4751994

Digital Object Identifier (DOI)

  • 10.1146/annurev-physiol-021115-105238

PubMed ID

  • 26527186

Additional Document Info

start page

  • 481

end page

  • 504


  • 78