<p>Microglia and astrocytes are the primary glial cells in the central nervous system (CNS) and their function is shaped by multiple factors. Regulation of CNS glia by the microbiota have been reported, although the role of specific bacteria has not been identified. We colonized germ-free mice with the type strain <i>Akkermansia muciniphila (Am</i>^T) and a novel <i>A. muciniphila</i> strain BWH-H3 (<i>Am-</i>H3) isolated from a subject with multiple sclerosis and compared to mice colonized with <i>Bacteroides cellulosilyticus</i> strain BWH-E5 (<i>Bc</i>) isolated from a healthy control subject. We then investigated the effect of these bacteria on microglia and astrocyte gene expression by RNA sequencing. We found altered gene expression profiles in brain microglia, with <i>Akkermansia</i> downregulating genes related to antigen presentation and cell migration. Furthermore, we observed strain specific effects, with <i>Akkermansia</i> H3 upregulating histone and protein binding associated genes and downregulating channel and ion transport genes. Astrocyte pathways that were altered by <i>Akkermansia</i> H3 mono-colonization included upregulation of proliferation pathways and downregulation in cytoskeletal associated genes. Furthermore, animals colonized with type strain <i>Akkermansia</i> and strain H3 had effects on the immune system including elevated splenic γδ-T cells and increased IFNγ production in CD4 + T cells. We also measured intestinal short chain fatty acids and found that both <i>A. muciniphila</i> strains produced proprionate while <i>B. cellulosilyticus</i> produced acetate, proprionate, and isovalerate. Taken together, our study shows that specific members of the intestinal microbiota influence both microglial and astroyctes which may be mediated by changes in short chain fatty acids and peripheral immune signaling.</p>