A longitudinal study of the pulmonary mycobiome in subjects with and without chronic obstructive pulmonary disease.

BACKGROUND: Few studies have examined the stability of the pulmonary mycobiome. We report longitudinal changes in the oral and pulmonary mycobiome of participants with and without COPD in a large-scale bronchoscopy study (MicroCOPD). METHODS: Repeated sampling was performed in 30 participants with and 21 without COPD. We collected an oral wash (OW) and a bronchoalveolar lavage (BAL) sample from each participant at two time points. The internal transcribed spacer 1 region of the ribosomal RNA gene cluster was PCR amplified and sequenced on an Illumina HiSeq sequencer. Differences in taxonomy, alpha diversity, and beta diversity between the two time points were compared, and we examined the effect of intercurrent antibiotic use. RESULTS: Sample pairs were dominated by Candida. We observed less stability in the pulmonary taxonomy compared to the oral taxonomy, additionally emphasised by a higher Yue-Clayton measure in BAL compared to OW (0.69 vs 0.22). No apparent effect was visually seen on taxonomy from intercurrent antibiotic use or participant category. We found no systematic variation in alpha diversity by time either in BAL (p-value 0.16) or in OW (p-value 0.97), and no obvious clusters on bronchoscopy number in PCoA plots. Pairwise distance analyses showed that OW samples from repeated sampling appeared more stable compared to BAL samples using the Bray-Curtis distance metric (p-value 0.0012), but not for Jaccard. CONCLUSION: Results from the current study propose that the pulmonary mycobiome is less stable than the oral mycobiome, and neither COPD diagnosis nor intercurrent antibiotic use seemed to influence the stability.

The pulmonary mycobiome-A study of subjects with and without chronic obstructive pulmonary disease.

BACKGROUND: 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). METHODS: 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. RESULTS: 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. CONCLUSION: Oral and pulmonary samples differed in taxonomic composition and diversity, possibly indicating the existence of a pulmonary mycobiome.

Motivation and response rates in bronchoscopy studies.

BACKGROUND: Bronchoscopy is frequently used to sample the lower airways in lung microbiome studies. Despite being a safe procedure, it is associated with discomfort that may result in reservations regarding participation in research bronchoscopy studies. Information on participation in research bronchoscopy studies is limited. We report response rates, reasons for non-response, motivation for participation, and predictors of participation in a large-scale single-centre bronchoscopy study ("MicroCOPD"). METHODS: Two hundred forty-nine participants underwent at least one bronchoscopy in addition to being examined by a physician, having lung function tested, and being offered a CT scan of the heart and lungs (subjects > 40 years). Each participant was asked an open question regarding motivation. Non-response reasons were gathered, and response rates were calculated. RESULTS: The study had a response rate just above 50%, and men had a significantly higher response rate than women (56.5% vs. 44.8%, p = 0.01). Procedural fear was the most common non-response reason. Most participants participated due to perceived personal benefit, but a large proportion did also participate to help others and contribute to science. Men were less likely to give exclusive altruistic motives, whereas subjects with asthma were more likely to report exclusive personal benefit as main motive. CONCLUSION: Response rates of about 50% in bronchoscopy studies make large bronchoscopy studies feasible, but the fact that participants are motivated by their own health status places a large responsibility on the investigators regarding the accuracy of the provided study information.

The Bergen COPD microbiome study (MicroCOPD): rationale, design, and initial experiences.

BACKGROUND: Recent methodological developments, in particular new sequencing methods for bacterial RNA/DNA, have shown that microorganisms reside in airways that do not suffer from acute infection and that respiratory microbiota might vary according to airways disease status. We aim to establish high-quality sampling methods for lower airways microbiota as well as describe the respiratory microbiome in subjects with and without chronic obstructive pulmonary disease (COPD) and to relate the microbiome to disease development, progression, and the host immune system. METHODS: The Bergen COPD microbiome study (MicroCOPD) is a longitudinal study aiming to collect data from 200 subjects with COPD as well as 150 individuals without COPD. At baseline, subjects go through a bronchoscopy in which protected specimen brushes, small-volume lavage, bronchoalveolar lavage, and bronchial biopsies provide a unique chance to analyze the microbiota and the host immune system status. These variables will be related to baseline clinical parameters (lung function, smoking status, exacerbation frequency, arterial blood gases, comorbidities, and medications) as well as follow-up parameters (lung function changes, exacerbation frequency, mortality, and more). RESULTS: Per date more than 150 bronchoscopies have been performed, equally distributed between cases and controls, with a very low complication frequency. CONCLUSIONS: MicroCOPD will provide unique data on a large material, with insight on a new field of respiratory research.