Fig. 4. Fecal microbial composition and PTE.

(A) Microbial alpha diversity was assessed by the Shannon index of richness and evenness. Mixed effects models were use with PTE status (EPILEPSY YES and NO), timepoint, and PTE status:timepoint interaction as fixed effects and rat identifier as a random effect. (B) Beta diversity analysis was performed using Bray-Curtis dissimilarity and visualized by principal coordinates (P1 and P2) analysis (PCoA). Each dot represents individual sample differently colored for the PTE status. Symbols denote different timepoints. P-values were calculated by repeated measures aware PERMANOVA including PTE status, timepoint, and PTE status:timepoint interaction. (C) Microbes that were differently abundant prior to LFPI, in rats that proceeded to develop and not develop PTE after LFPI. Samples were analyzed together in mixed effects models implemented in MaAsLin2 with PTE status and timepoint as fixed effects and rat identifier as a random effect. Interaction with time was not included as this was not significant in the beta diversity analysis. Shown are ASVs associated with PTE (q<0.25), with bold font indicating ASVs with q<0.05 and italics font indicating ASVs with q between 0.05 and 0.1. Effect size is shown as the log2 of the fold change. Dot sizes are proportional to mean ASV abundance and dot colors represent different phyla.