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Abstract

Cystic fibrosis (CF) is a common fatal genetic disorder with mortality most often resulting from
microbial infections of the lungs. Culture-independent studies of CF-associated microbial
communities have indicated that microbial diversity in the CF airways is much higher than
suggested by culturing alone. However, these studies have relied on indirect methods to sample the
CF lung such as expectorated sputum and bronchoalveolar lavage (BAL). Here, we characterize the
diversity of microbial communities in tissue sections from anatomically distinct regions of the CF
lung using barcoded 16S amplicon pyrosequencing. Microbial communities differed significantly
between different areas of the lungs, and few taxa were common to microbial communities in all
anatomical regions surveyed. Our results indicate that CF lung infections are not only polymicrobial,
but also spatially heterogeneous suggesting that treatment regimes tailored to dominant
populations in sputum or BAL samples may be ineffective against infections in some areas of
the lung