The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation

Lisa A Carmody, Jiangchao Zhao, Linda M Kalikin, William LeBar, Richard H Simon, Arvind Venkataraman, Thomas M Schmidt, Zaid Abdo, Patrick D Schloss, John J LiPuma

Recent work indicates that the airways of persons with cystic fibrosis (CF) typically harbor complex bacterial communities. However, the day-to-day stability of these communities is unknown. Further, airway community dynamics during the days corresponding to the onset of symptoms of respiratory exacerbation have not been studied. Using 16S rRNA amplicon sequencing of 95 daily sputum specimens collected from four adults with CF, we observed varying degrees of day-to-day stability in airway bacterial community structures during periods of clinical stability. Differences were observed between study subjects with respect to the degree of community changes at the onset of exacerbation. Decreases in the relative abundance of dominant taxa were observed in three subjects at exacerbation. We observed no relationship between total bacterial load and clinical status and detected no viruses by multiplex PCR. CF airway microbial communities are relatively stable during periods of clinical stability. Changes in microbial community structure are associated with some, but not all, pulmonary exacerbations, supporting previous observations suggesting that distinct types of exacerbations occur in CF. Decreased abundance of species that are dominant at baseline suggests a role for less abundant taxa in some exacerbations. Daily sampling revealed patterns of change in microbial community structures that may prove useful in the prediction and management of CF pulmonary exacerbations.