Multiple sclerosis (MS) is an autoimmune disease of the central nervous system. The etiology of MS is multifactorial, with disease risk determined by genetics and environmental factors. An emerging risk factor for immune-mediated diseases is an imbalance in the gut microbiome. However, the identity of gut microbes associated with disease risk, their mechanisms of action, and the interactions with host genetics remain obscure. To address these questions, we utilized the principal autoimmune model of MS, experimental autoimmune encephalomyelitis (EAE), together with a genetically diverse mouse model representing 29 unique host genotypes, interrogated by microbiome sequencing and targeted microbiome manipulation. We identified specific gut bacteria and their metabolic functions associated with EAE susceptibility, implicating short-chain fatty acid metabolism as a key element conserved across multiple host genotypes. In parallel, we used a reductionist approach focused on two of the most disparate phenotypes identified in our screen. Manipulation of the gut microbiome by transplantation and cohousing demonstrated that transfer of these microbiomes into genetically identical hosts was sufficient to modulate EAE susceptibility and systemic metabolite profiles. Parallel bioinformatic approaches identified Lactobacillus reuteri as a commensal species unexpectedly associated with exacerbation of EAE in a genetically susceptible host, which was functionally confirmed by bacterial isolation and commensal colonization studies. These results reveal complex interactions between host genetics and gut microbiota modulating susceptibility to CNS autoimmunity, providing insights into microbiome-directed strategies aimed at lowering the risk for autoimmune disease and underscoring the need to consider host genetics and baseline gut microbiome composition.

Gut commensal bacteria exert profound effects on the immune system of the mammalian host. In particular, Lactobacillus species have a long-standing history as putative probiotics, generally being characterized as safe and/or beneficial for the mammalian host. Despite this fact, current literature points to both pro- and anti-inflammatory roles for this genus, with little consensus as to the mechanisms governing these divergent outcomes. Using mouse models, we and others have previously shown that, unexpectedly, stable commensal colonization with Lactobacillus reuteri (L. reuteri) is correlated with, and sufficient to enhance host susceptibility to experimental autoimmune encephalomyelitis (EAE), in association with alterations in tryptophan derived metabolites in host circulation. To identify the underlying mechanisms, we characterized the genomes of commensal L. reuteri isolates, along with two other representative Lactobacillus species, L. murinus and L. johnsonii. Whole genome sequencing revealed an enrichment in the enzymatic machinery necessary to catabolize dietary tryptophan into immunomodulatory indole derivatives in L. reuteri. Mechanistically, supplementation with high dietary tryptophan sustained an L. reuteri-dependent exacerbation of EAE and augmented inflammatory T cell populations, while depletion of dietary tryptophan profoundly suppressed EAE in a microbiome-specific manner. Taken together, our data reveal considerable variation in the genetic landscape of commensal Lactobacilli, and demonstrate mechanisms responsible for differential modulation of autoimmunity by gut microbiota, including an unexpected disease-promoting role for catabolism of host dietary tryptophan.