Figure 3.

Changes in metacommunity diversity across the disease periods. Given are the whole microbiota, core and rare OTUs groups. Disease periods are denoted by (B₀) baseline pre-CFPE; (E) CFPE, 30 days prior to treatment; (T) treatment for clinical exacerbation; (R) recovery, 30 days post-CFPE treatment; and (B₁) baseline post-CFPE. Richness (S*) was calculated with a uniform re-sample size following 1000 iterations in each instance; re-sample sizes by group were n=55 656 (whole), n=47 092 (core), and n=8712 (rare) equating to the lowest number of sequences by disease period within each group. Error bars represent the standard deviation of the mean. Asterisks denote significant differences between B₀ and subsequent disease periods at the P<0.05 level and determined by two sample t-tests.