16S rRNA sequencing of sputum from individuals with CF and non-CF bronchiectasis with underlying fungal disease.. Bacterial and fungal microbiota associated with fungal disease in cystic fibrosis and bronchiectasis

Objectives: Application of next generation sequencing (NGS) technologies have lead to the importance of bacterial communities in disease progression being recognised in Cystic Fibrosis (CF) and non-Cystic Fibrosis Bronchiectasis (BX). The fungal microbiome and how fungal and bacterial communities relate to one another, however is less well understood and is the focus of the present study.Methods: Quantitative PCR and next generation sequencing of ITS2 and the 16S rRNA gene were carried out on sputum DNA from 85 CF and 24 with BX adults with underlying fungal disease including ABPA and fungal bronchitis. High quality bacterial and fungal reads for analysis were generated from all subjects. Fungal and bacterial communities were analysed in R (Version 3.5.0). Results: No correlation was observed between bacterial and fungal abundance using qPCR and no significant differences in the bacterial community was observed with treatment (systemic steroids, antibiotics or antifungals). Both bacterial and fungal communities were found to be significantly (P>0.001) more diverse in BX than in CF. Significant differences in bacterial composition were observed between different fungal disease groups. Despite this, using the Mantel test no significant correlations were observed between bacterial and fungal OTUs (Operational Taxonomic Units). No significant correlations were observed between Pseudomonas and any Aspergillus OTUs. Conclusion: Whilst changes in bacterial diversity were clearly seen between the fungal disease cohorts, this was independent of treatment and no significant correlations were found. Our results demonstrate that presence of fungal disease influences the bacterial communities composition, but that there is no community level relationship between bacteria and fungi in this cohort.