Structure of the gut microbiome of EAE induced B6 mice

EAE is a mouse model that is widely used to understand MS pathogenesis. Our findings that gut inflammation is enhanced, and the composition of the microbial community is altered, in mice that are inoculated with specific bacteria represented in PwMS suggested that mice induced with EAE may have similar gut microbial changes, the findings of which could uncover novel gut microbial biomarkers. Therefore, to identify microbial changes in mice induced with EAE, we first characterized the gut microbiome in EAE-induced mice compared to control mice. Mice were divided into three groups (n=5 /group) according to the following treatment: control (PBS), vehicle control (CFA+PTX), or induced with EAE (MOG35-55+CFA+PTX). To investigate the gut microbiota changes, we collected fecal samples and colonic mucosal samples, isolated DNA, and performed shotgun metagenomic sequencing. Mice induced with EAE (i.e., treated with MOG35-55) had a differential abundance of Akkermansia species including A. muciniphila and Akkermansia sp. CAG:344, whereas Bifidobacterium species including B. pseudolongum, B. cuniculi, B. animalis, B. choerinum and Bifidobacterium sp. AGR2158 were differentially abundant in vehicle control group. For the vehicle control-treated and MOG35-55-treated groups, A. muciniphila and B. pseudolongum were differentially abundant in the mucosal layer at the species level whereas Akkermansia and Bifidobacterium were the only two bacteria associated with the mucosal layer at the genus level. Identification of bacteria associated with EAE induced mice will help to understand the role of microbiome in EAE and MS as a whole.