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.