We aimed to examine airway microbiota changes in steady state and during exacerbations, in adults with non-cystic fibrosis (CF) bronchiectasis. 

Adults with non-CF bronchiectasis were enrolled consecutively between 2021 and 2022. Nasopharyngeal swabs (URT) and spontaneous sputum samples (LRT) were collected at baseline, 3 and 6 months of follow-up, and when possible, during exacerbation. Samples were analyzed using cultures for bacteria, mycobacteria and fungi. 16S rRNA gene amplicon sequencing and quantitative PCR were performed to assess bacterial communities and microorganisms. 

Eighteen subjects (11 exacerbations) were included (49 LRT and 41 URT samples). LRT and URT samples presented significantly different variance and composition of the microbial communities. LRT showed larger variation of beta-diversity over time in subjects with post-infectious disease, compared to the rest of the cohort. During the study period, the evenness and richness of the microbiota did not show significant variation, but in the three months after exacerbation (and treatment), the evenness increased in LRT and the richness increased in URT, albeit with limited statistical significance due to the few exacerbations. The most commonly detected pathogen was H. influenzae in exacerbators, and P. aeruginosa in non exacerbators. 

Microbiota in patients with non-CF bronchiectasis displayed a wide variety of bacteria by conventional cultures and different trajectories of the microbial communities over time. Improved understanding of microbiota changes in bronchiectasis may enhance our understanding of mechanisms leading to exacerbations and provide potential strategies for their mitigation.