Aim: To investigate whether the compositionality of the lower airway microbiota predicts later exacerbation risk in persons with COPD in a cohort study.

Materials and methods: We collected lower airways microbiota samples by bronchoalveolar lavage and protected specimen brushes, and oral wash samples from 122 participants with COPD. Bacterial DNA was extracted from all samples, before we sequenced the V3-V4 region of the 16S RNA gene. The frequency of moderate and severe COPD exacerbations was surveyed in telephone interviews and in a follow-up visit. Compositional taxonomy and alpha and beta diversity were compared between participants with and without later exacerbations. 

Results: The four most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria and Fusobacteria in both groups, and the four most abundant genera were Streptococcus, Veillonella, Prevotella and Gemella. The relative abundances of different taxa showed a large variation between samples and individuals, and no statistically significant difference of either compositional taxonomy, or alpha or beta diversity could be found between participants with and without COPD exacerbations within follow-up. 

Conclusion: The findings from the current study, indicate that individual differences in the lower airway microbiota in persons with COPD far outweigh group differences between frequent and non-frequent COPD exacerbators, and that the compositionality of the microbiota is so complex as to present large challenges for use as a biomarker of later exacerbations. 

The dataset is part of the larger Bergen COPD Microbiome Study ("MicroCOPD"), and the processing is well described in the paper & supplement.

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