Genus-level dynamics over time. A mixed-effects model was built for each genus in the form of relative abundance ∼ interval + 1|patient ID, with the interval defined according to Figure 1A. Horizontal lines represent q = 0.05. The significance of the regression coefficient for interval was estimated from 200 bootstraps, corrected for multiple testing by the Benjamini-Hochberg method, plotted along the y-axis, and used to determine whether the relative abundance of a genus changed between the intervals. The regression coefficient for interval was plotted along the x-axis. Points to the right (left) of the vertical line represent increased (decreased) genera at short-term 2 (ST2; panel A) or long-term (LT; panel B) relative to short-term 1 (ST1).