Figure 1

Gut microbe community shows minimal changes during early-phase EAE (A). Stool sample collection strategy and EAE clinical scores over time. (B) Shannon, richness and phylogenetic diversity over the time course. One-way ANOVA (F = (4,29), *p < 0.05, **p < 0.01, ***p < 0.0001) (C). One-way ANOVA with Dunnett’s post-test comparing each group against baseline (DPI -14) weighted UniFrac distances (*p < 0.05, ***p < 0.001). Each circle represents a specific OTU (n = 91). (D) Normalized relative abundance stacked bar chart of top 16 microbes over days suggest the greatest deviations in OTU abundances occurred on DPI -14 and DPI 3. In particular, a substantial increase was noted in the order Clostridia (pink) on DPI -14 and a loss of the genus Lactobacillus (purple) on DPI 3. (E) Principle component analysis using significantly altered microbes (p < 0.01) reveal contributors to pre- and post-immunization state separation. (F) Two-way ANOVA of Candidatus arthromitus reveals no differences in abundance between mildly and severely affected mice (p = 0.86, (F) (1, 26) = 0.03139 Dunn’s non-parametric test, Kruskal-Wallis test). (G) Analysis of OTUs grouped under the genus Lactobacillus (**p < 0.01, Dunn’s non-parametric test, Kruskal-Wallis test = 17.76) and the species Lactobacillus reuteri (*p = 0.0138, Dunn’s non-parametric test, Kruskal-Wallis test = 11.01).