A study of the airway mycobiome in COPD patients and controls

Background: We aimed to explore the so far unknown role of the pulmonary mycobiome in COPD and asthma patients compared to controls. Methods: In addition to oral wash (OW) and negative control samples, bronchoalveolar lavage (BAL) was collected through a sterile catheter during bronchoscopies in the Bergen MicroCOPD study. We used QIIME2 and the R package decontam for bioinformatic analyses. UNITE databases were used to assign taxonomy. Results: We obtained samples from 95 COPD and 13 asthma patients, and 100 healthy controls. 66% were ex-smokers, mean age was 66.3, and 60% of COPD patients, and 69% of asthma patients, used inhaled corticosteroids (ICS). After removal of likely contaminants and low-abundance taxa, 410 samples and 13x106 sequences remained. Malassezia was the most frequent genus in control samples from BAL, while Candida dominated in COPD and asthma samples, figure 1. α diversity differed between OW and BAL samples (p=0.003), but not by study group, sex, or use of ICS. β diversity differed by sample type (p=0.001), and between asthma patients and controls (p=0.002) and COPD (p=0.003). Conclusion: Candida and Malassezia were the most abundant fungal genera in BAL samples. Fungal alpha and beta diversity differed between OW and BAL, possibly indicating the existence of a respiratory mycobiome. There was a difference in β diversity between asthma patients and the other subjects, indicating an assocation between mycobiome and diseases.