For many years, the human lower airways were considered a sterile environment where the presence of microorganisms was interpreted as an abnormal health state. Not anymore.
High-throughput sequencing-based studies have led to a shift in this perception. Even in healthy conditions the lower airways show either a transient presence or a permanent colonization by microorganisms.
This review summarizes the methodology pertinent to high-throughput sequencing studies, based on amplicon sequencing, and discusses good practices and common pitfalls: http://www.waojournal.org/content/8/1/23
The study of the human lower airway microbiome is still in its infancy.
The microbiome of the human lower airways: a next generation sequencing perspective.
Velma T. E. Aho et al. World Allergy Organization Journal 2015, 8:23, free full text.
Image source: Lungs, Wikipedia, public domain.
As some of you know, I have been the Editor of the World Allergy Organization (WAO) Small Airways Working Group "What's New?" monthly summary since 2011. The summary features the top 3 asthma/small airways articles each month. The article above is part of the project. The archive is here: http://www.worldallergy.org/small_airways_group/reviews/archive.php