Fig. 1

Changes in microbiota composition during EAE. Mice were immunized with MOG, and feces were collected prior to EAE induction at −22, −21, −20, −18, −14, and −6 days post immunization (DPI), on the day of immunization prior to EAE induction at 0 DPI and post EAE induction at 3, 8, 15, and 29 DPI. A Schematic design showing the 11 time points for fecal samples collection. B Mean EAE clinical scores overtime. Results are presented as mean ± SEM (n = 11 mice). C α-Diversity metrics for Shannon diversity, Observed species, and Faith’s diversity were calculated at an average sampling depth of 1500 reads per sample. No significant differences were observed for any of the diversity estimators analyzed (mixed-effect model followed by Dunnett’s test). D Principal coordinate analysis of intestinal microbiota samples based on Bray-Curtis. Each dot represents the microbiota from one mouse. E Taxa plots showing compositional differences in fecal microbiota in mice at the indicated time points. F Linear discriminant analysis (LDA) effect size of significantly altered bacteria at the lowest classifiable levels at the indicated time points. G Relative abundance of selected species altered in EAE mice at the indicated time points. Results are presented as mean ± SEM (n = 11 mice), *p < 0.05; **p < 0.01; ***p < 0.001. OTU, operational taxonomic unit; numbers in parenthesis represent OTU. EC1, Enterococcus canintestini/canis/dispar/durans/faecalis/faecium/hirae/lactis/mundtii/ratti/rivorum/villorum