Summary of GLMM results from 29 modules with significant time by group interaction. Summary of GLMM results from 29 modules with significant time by group interaction. (A) The quantity plotted is the predicted marginal mean (PMM) of the slope coefficients. Significance testing was done by comparing goodness-of-fit values from full and reduced GLMM specifications, and the full model was used to produce the PMM estimates shown here. This quantity was primarily calculated to get a succinct summary of the direction of temporal change and does not always coincide with the interaction coefficient that is the focus of the main analysis. The estimates were obtained by running the lstrends function from the lsmeans R package (134). (B) The underlying KO abundance trajectories of a significant module (M00031; lysine biosynthesis) that decreases in abundance in DNR mice and increases in abundance in WT mice over time, as evidenced by a negative model slope and a positive model slope, respectively. (C) The plot was constructed as described for panel B, except that this significant module (M00330; adhesin transport) significantly increased in abundance over time in DNR mice whereas it did not change in abundance in WT mice. For both panel B and panel C, the shaded ribbons represent LOESS confidence bounds. Thomas Sharpton et al. mSystems 2017; doi:10.1128/mSystems.00036-17