Original Article|Articles in Press

Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis

Published:February 21, 2023DOI:


      • Absolute abundance of fungi differed significantly among CF sputa; therefore, qPCR corrected abundance to account for total fungal abundance may be valuable for mycobiome studies.
      • Members of the Candida genus are highly abundant in sputa of adults with cystic fibrosis and are associated with pulmonary exacerbation state.
      • Higher lung function is associated with greater fungal richness and alpha-diversity and CFTR modulator use is associated with greater fungal alpha-diversity; whereas chronic azithromycin use is associated with lower fungal richness and alpha-diversity.



      The respiratory tract fungal microbiome in cystic fibrosis (CF) has been understudied despite increasing recognition of fungal pathogens in CF lung disease. We sought to better understand the fungal communities in adults with CF, and to define relationships between fungal profiles and clinical characteristics.


      We enrolled 66 adults with CF and collected expectorated sputum, spirometry, Cystic Fibrosis Questionnaire-revised, and clinical data. Fungi were molecularly profiled by sequencing of the internal transcribed spacer (ITS) region. Total fungal abundance was measured by quantitative PCR. Relative abundance and qPCR-corrected abundances were determined. Selective fungus culture identified cultivable fungi. Alpha diversity and beta diversity were measured and relationships with clinical parameters were interrogated.


      Median age was 29 years and median FEV1 percent predicted 58%. Members of the Candida genus were the most frequent dominant taxa in CF sputum. Apiotrichum, Trichosporon, Saccharomyces cerevisiae, and Scedosporium were present in high relative abundance in few samples; whereas, Aspergillus species were detected at low levels. Higher FEV1% predicted and CFTR modulator use were associated with greater alpha-diversity. Chronic azithromycin use was associated with lower alpha-diversity. Patients with acute pulmonary had distinct fungal community composition compared to clinically stable subjects. Differing yeast species were mainly responsible for the community differences.


      The respiratory tract fungal microbiome in adults with CF is associated with lung function, pulmonary exacerbation status, macrolide use, and CFTR modulator use. Future work to better understand fungal diversity in the CF airway and its impact on lung health is necessary.



      FEV1 (forced expiratory volume in one second), CFQ-R (cystic fibrosis questionnaire-revised), DTT (dithiothreitol), ITS (internal transcribed spacer), QPCR (quantitative polymerase chain reaction), OTU (operational taxonomic unit), CFTR (cystic fibrosis transmembrane conductance regulator), ABPA (allergic bronchopulmonary aspergillosis), IV (intravenous), BAL (bronchoalveolar lavage)
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