Fig. 3

Effect of vancomycin on alpha and beta diversity during EAE. A Alpha diversity metrics for Shannon diversity, Observed species, and Faith’s diversity were calculated at an average sampling depth of 1500 reads per sample in single-treatment housed untreated mice (control), single-treatment housed vancomycin mice (vancomycin), untreated mice cohoused with vancomycin-treated mice (ControlCoho), and vancomycin-treated mice cohoused with untreated mice (VancoCoho). Results are expressed as mean ± SEM (n = 11–12 mice/group). Statistical comparisons are made using one-way ANOVA followed by Tukey test. *Significant difference with control group (p < 0.05), +significant difference with vancomycin group (p < 0.05), and #significant difference with control-cohoused group (p < 0.05). B Principal coordinate analysis of intestinal microbiota samples based on Bray-Curtis shows significantly different clustering between control and vancomycin (q < 0.003), ControlCoho and vancomycin (q < 0.002), VancoCoho and control (q < 0.002) at all time points, vancomycin and VancoCoho (q < 0.002), control and ControlCoho (q < 0.002) starting at −6 DPI, and VancoCoho and ControlCoho (q < 0.005) at −21, −6, and 0 DPI but not at 3, 8, 15, and 29 DPI. q = PERMANOVA p-values adjusted for false discovery rate. Each dot represents the microbiota from one mouse. C Taxa plots showing compositional differences in fecal microbiota at the indicated time points in control, vancomycin, ControlCoho, and VancoCoho mice. EC1, Enterococcus canintestini/canis/dispar/durans/faecalis/faecium/hirae/lactis/mundtii/ratti/rivorum/villorum