Microbial community composition in explanted cystic fibrosis (CF) and unused donor lungs Raw sequence reads. Microbial community composition in explanted cystic fibrosis (CF) and unused donor lungs

We determined if the lung microbiota in end-stage cystic fibrosis (CF) varied within and between patients, was spatially heterogeneous and related to localized structural damage.Tissue and airway luminal mucus samples were extracted from explanted lungs of CF patients (n=11) and unused donor lungs (n=4). Microbial community composition was determined by Illumina MiSeq sequencing and related to the CF-Computed tomography (CT) score and features of end-stage lung disease on micro-CT.Ninety-eight CF tissue samples (n=11 patients), 20 CF luminal mucus samples (n=8 patients) and 33 donor tissue samples (n=4 patients) were analysed. Significant differences in microbial community composition were apparent between the 3 groups. However, there was some overlap between the three communities, particularly between CF and donor tissue and CF tissue and CF luminal mucus. Microbial richness, diversity and evenness were all significantly less in CF luminal mucus compared to CF tissue, with dominance significantly higher in tissue. For both CF and donor tissue, significant intra- and inter-patient variability in ecological parameters was observed. No significant relationships were observed between ecological parameters and CF-CT score, or presence of features of end-stage lung disease.The end-stage CF lung is characterised by a low diversity microbiota, which differs markedly within and between individual CF patients. Moreover, diversity and richness in deeper airway tissue is underestimated by analysis of luminal mucus. There was no clear relationship between regional variation and structural lung damage. Larger, longitudinal omics-based studies may facilitate increased insight into the relationship between microbiota composition and structural damage in CF.