Abstract
The fungal part of the pulmonary microbiome (mycobiome) is understudied. We report the composition of the oral and pulmonary mycobiome in participants with COPD compared to controls in a large-scale single-centre bronchoscopy study (MicroCOPD). Oral wash and bronchoalveolar lavage (BAL) was collected from 93 participants with COPD and 100 controls. Fungal DNA was extracted before sequencing of the internal transcribed spacer 1 (ITS1) region of the fungal ribosomal RNA gene cluster. Taxonomic barplots were generated, and we compared taxonomic composition, Shannon index, and beta diversity between study groups, and by use of inhaled steroids. The oral and pulmonary mycobiomes from controls and participants with COPD were dominated by Candida, and there were more Candida in oral samples compared to BAL for both study groups. Malassezia and Sarocladium were also frequently found in pulmonary samples. No consistent differences were found between study groups in terms of differential abundance/distribution. Alpha and beta diversity did not differ between study groups in pulmonary samples, but beta diversity varied with sample type. The mycobiomes did not seem to be affected by use of inhaled steroids. Oral and pulmonary samples differed in taxonomic composition and diversity, possibly indicating the existence of a pulmonary mycobiome.
Highlights
Fungi are ubiquitous, and are found in indoor and outdoor environments [1]
We report the composition of the oral and pulmonary mycobiome in participants with chronic obstructive pulmonary disease (COPD) compared to controls in a large-scale single-centre bronchoscopy study (MicroCOPD)
The oral and pulmonary mycobiomes from controls and participants with COPD were dominated by Candida, and there were more Candida in oral samples compared to bronchoalveolar lavage (BAL) for both study groups
Summary
Due to its direct communication with surrounding air, the respiratory tract is constantly exposed to fungal spores through inhalation [2]. The fungal part of the microbiome, the mycobiome, of the lungs is understudied [3], and only three studies have used generation sequencing to study the mycobiome of the respiratory tract in COPD [4,5,6]. Mycobiome studies of other respiratory diseases have evolved rapidly. There is clearly a need for large studies of the mycobiome, with a well-characterised COPD disease population and healthy controls. The fungal part of the pulmonary microbiome (mycobiome) is understudied. We report the composition of the oral and pulmonary mycobiome in participants with COPD compared to controls in a large-scale single-centre bronchoscopy study (MicroCOPD)
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