Lungs of patients that have cystic fibrosis (CF) provide a unique environment for microbial communities. We investigated the microbial community structure found in pharyngeal samples taken from 45 patients with CF. Relative abundances of 2079 microbial taxa were obtained using taxon specific primers on a 16S rRNA gene microarray (PhyloChip).

Results/Conclusions

Species richness increased with increasing total abundance of bacterial species, but was generally lower in patients identified to have Pseudomonas aeruginosa and who had received antibiotic treatments. There were no relationships of bacterial species richness to age, sex, or patient lung function. Beta diversity was higher when comparing patients with and without P. aeruginosa than when comparing uninfected patients with one another. That is, colonization of CF lungs by P. aeruginosa leads to distinctively different communities. Patients heterozygous or homozygous for the most common CF genotype had higher species richness of bacteria than those with rarer genotypes, suggesting that different CF genotypes provide very different environments for colonization by bacteria. Using a neutral model for community dynamics that assumes different colonization rates for different taxa to estimate average colonization rates for each patient, we found a negative relationship between species richness and the susceptibility of patients to colonization. These results may contribute to new strategies for managing CF patient treatment regimes in the future.