Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis

Sci Rep. 2020 Feb 27;10(1):3589. doi: 10.1038/s41598-020-60015-4.


Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acute Disease
  • Adult
  • Aspergillus / physiology*
  • Candida / physiology*
  • Cystic Fibrosis / microbiology*
  • Disease Progression
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Lung / microbiology*
  • Male
  • Microbiota / genetics*
  • Pseudomonas / physiology*
  • RNA, Ribosomal, 16S / genetics*
  • Respiratory Tract Infections / microbiology*
  • Scedosporium / physiology*
  • Sequence Analysis, DNA
  • Sputum / microbiology
  • Young Adult


  • RNA, Ribosomal, 16S