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Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis
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Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis
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Journal Article
Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis
2020
Overview
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.
Publisher
Nature Publishing Group UK,Nature Publishing Group
Subject
/ 45/47
/ 45/77
/ Adult
/ Cystic Fibrosis - microbiology
/ Female
/ High-Throughput Nucleotide Sequencing
/ Humanities and Social Sciences
/ Humans
/ Male
/ Microbiology and Parasitology
/ Mycology
/ Niches
/ Pulmonology and respiratory tract
/ Respiratory Tract Infections - microbiology
/ RNA, Ribosomal, 16S - genetics
/ rRNA
/ Science
