FIG 3.

(A) Volcano plots indicating taxa that are significantly increased (upper right quadrant) or decreased (upper left quadrant) in the pairwise comparisons indicated, using moderated t-test models (R package limma). Results shown are from analyses of all subjects. Dashed lines, significant false discovery rate-adjusted P values and changes in relative abundance of at least 2-fold, or log₂ equal to 1. Taxa exhibiting significant changes are colored by phylum-level classification, as shown. Note that in addition to the highlighted taxa, many other microbiota members exhibited smaller-scale changes in abundance, which cumulatively may contribute importantly to microbiome community function, (B) Changes in the relative abundance of taxa from Exac to Post1 and Post1 to Post2, segregated by type of exacerbation treatment (antibiotics only, systemic corticosteroids only, or both; n = 4 subjects in each treatment group).