Investigations of the Microbial Communities of the Respiratory Tract in the Elderly and in Cystic Fibrosis via Culture-Dependent and -Independent Approaches

Abstract

The human microbiota is the collection of microorganisms which live on and in the human body. These organisms have been implicated in a host of diseases and disorders and nationwide initiatives have helped us understand their heterogeneity across the population in health. In this work, I investigate the respiratory tract microbiota and its correlations in age and disease. Elderly (≥ 65 years of age) are at a greater risk of respiratory infection; previous studies have shown changes to the elderly gut microbiota which correlate with the health of these individuals. Thus, we investigated the upper respiratory tract in comparison to mid-aged adults to identify statistically different communities within the anterior nares and oropharynx which may be associated with increased respiratory infection risk in this population. Individuals with cystic fibrosis have a lung microbiota which contributes to the onset of pulmonary exacerbations, increased inflammation, which is the greatest cause of patient mortality. However, it is not understood what triggers these events. In this work, we used 16S rRNA gene sequencing to longitudinally identify the lung microbiota in a subset of patients but were unable to identify any consistent correlations in the lung microbiota and pulmonary exacerbation onset. In order to gain a better resolution of these communities, we combined culture-independent sequencing technology with culture-enrichment. We showed that 81.21% of OTUs representing 99.15% of the biomass of the cystic fibrosis lung is culturable and that metagenomic sequencing of these cultured communities provide better taxonomic resolution of the cystic fibrosis lung. Together, this work shows the contributions of the respiratory tract microbiota in age and disease.