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

We determined if the microbiota in the lungs of people with end-stage cystic fibrosis (CF) is spatially heterogeneous and related to localized structural damage. Tissue and airway sputum samples were extracted from explanted lungs of people with CF (n=11 patients) and unused donor lungs (n=4 patients). Microbial community composition was determined by Illumina MiSeq sequencing and related to the Brody score and features of end-stage lung disease on micro-CT.Ninety-eight CF tissue samples (n = 11 patients), 20 CF sputum 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 between CF tissue and CF sputum. Richness, diversity and evenness were all significantly lower in CF sputum compared to CF tissue with dominance significantly higher. 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 Brody 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 the deeper airway tissue is underestimated by analysis of sputum. 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.