Significant advances in culture-independent methods have expanded our knowledge
about the diversity of the lung microbial environment. Complex microorganisms
and microbial communities can now be identified in the distal airways in a variety of
respiratory diseases, including cystic fibrosis (CF) and the posttransplantation lung.
Although there are significant methodologic concerns about sampling the lung microbiome,
several studies have now shown that the microbiome of the lower respiratory
tract is distinct from the upper airway. CF is a disease characterized by chronic airway
infections that lead to significant morbidity and mortality. Traditional culture–dependent
methods have identified a select group of pathogens that cause exacerbations
in CF, but studies using bacterial 16S rRNA gene–based microarrays have shown that
the CF microbiome is an intricate and dynamic bacterial ecosystem, which influences
both host immune health and disease pathogenesis. These microbial communities
can shift with external influences, including antibiotic exposure. In addition, there
have been a number of studies suggesting a link between the gut microbiome and respiratory
health in CF. Compared with CF, there is significantly less knowledge about
the microbiome of the transplanted lung. Risk factors for bronchiolitis obliterans
syndrome, one of the leading causes of death, include microbial infections. Lung
transplant patients have a unique lung microbiome that is different than the pretransplanted
microbiome and changes with time. Understanding the host-pathogen interactions
in these diseases may suggest targeted therapies and improve long-term
survival in these patients. (Translational Research 2016;-:1–13)