A cohort study of the airway mycobiome in adult cystic fibrosis patients: differences in community structure of fungi compared to bacteria reveal predominance of transient fungal elements.
The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases but infection rates are much lower.
This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult cystic fibrosis (CF) patients during non-exacerbation periods and under continuous antibiotic treatment.
Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and ITS) and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were only detected at low frequencies. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients had been analysed. In contrast to bacteria, a large number of fungal species was observed together with high fluctuations over time and between patients. These findings demonstrated that the mycobiome was dominated by transient species. This strongly suggests that the main driving force is their presence in inhaled air rather than colonization.
Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF and colonisation by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungi-related disease progression in CF.