The lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation
Characterization of bacterial populations in infectious respiratory diseases will provide a better understanding of the relationship between the lung microbiota, disease pathogenesis and treatment outcomes. Objectives: To comprehensively define lung microbiota composition during stable disease and exacerbation in bronchiectasis patients using both strict anaerobic culture and massively parallel pyrosequencing. Methods: Sputum was collected from bronchietasis patients when clinically stable and before and after completion of antibiotic treatment of pulmonary exacerbations. Bacterial abundance and community composition were analyzed using culture and 16S rDNA pyrosequencing. Measurements and Main Results: In clinically stable patients, aerobic and anaerobic bacteria were detected in 40/40 (100%) and 33/40 (83%) sputum samples, respectively. The dominant organisms cultured were P. aeruginosa (n=10 patients), H. influenzae (n=12), S. aureus(n=6), Prevotella (n=18) and Veillonella (n=13). Pyrosequencing generated over 150,000 sequences, representing 113 distinct microbial taxa; the majority of observed community richness resulted from taxa present in low abundance with similar patterns of phyla distribution in clinically stable patients and patients at the onset of exacerbation. Following antibiotic treatment of exacerbation, there was no change in total (p=0.925), aerobic(p=0.917) or anaerobic (p=0.683) viable counts and only a limited shift in community composition. There was also no correlation between lung function and microbial community diversity (?=0.123, p=0.549). Conclusions: A complex microbiota is present in the lungs of patients with bronchiectasis. Bacterial density and community diversity remain stable through treatment of exacerbations which suggests that changes in lung microbiota composition do not account for pulmonary exacerbations in patients with bronchiectasis.