Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Cellular, Molecular and Biomedical Sciences

First Advisor

Dimitry N. Krementsov


Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system. The etiology of MS is complex and poorly understood; however, disease risk is likely combinatorial due to the effects of both genetics and environmental risk factors. A recently identified environment risk factor for MS is the gut microbiome. However, the specific gut microbiota associated with disease risk, onset and/or progression, their mechanisms of action, and impact of host genetics remain unclear. Leveraging the primary autoimmune mouse model of MS, experimental autoimmune encephalomyelitis (EAE), in a genetically diverse mouse model consisting of 29 unique genotypes, combined with gut microbial profiling, we identified specific bacteria and their metabolic functions associated with EAE susceptibility. Functional prediction and enrichment analysis correlated both short-chain fatty acid (SCFA) and amino acid metabolism with disease severity across multiple genotypes. Moreover, gut microbiome transplantation and cohousing studies revealed that transfer of disparate microbiomes into genetically identical hosts is sufficient to alter disease severity and modulate systemic metabolic profiles, highlighting a potential role of both SCFA and amino acid metabolism, in particular that of tryptophan. Moreover, we identified the putative probiotic and gut commensal Lactobacillus reuteri (L. reuteri) as associated with exacerbation of EAE, which was functionally confirmed through bacterial isolation and colonization studies. To understand the mechanisms of L. reuteri driven CNS autoimmunity, we characterized the genome of L. reuteri isolates, coupled with metabolomic profiling, modulation of dietary substrates, and microbiota manipulation. L. reuteri genomes were enriched in the enzymatic machinery necessary to metabolize dietary tryptophan into immunomodulatory indole derivatives. Further, metabolomic profiling of L. reuteri monocultures and the serum of L. reuteri-colonized mice were both depleted in kynurenines and enriched in a wide array of known and novel tryptophan derivatives, including indole acetate, indole-3-glyoxylic acid, tryptamine, p-cresol, and imidazole derivatives. Functionally, dietary tryptophan was required for L. reuteri-driven exacerbation of CNS autoimmunity and depletion of dietary tryptophan was sufficient to suppress disease activity and inflammation within the CNS. In vitro experiments demonstrated that L. reuteri tryptophan-derived metabolites functionally served as agonists or antagonists of the immunomodulatory aryl hydrocarbon receptor to enhance T cell production of IL-17. Our data underscore the interplay between host genetics and commensal gut microbiota in predisposition to CNS autoimmunity, demonstrating that commensal microbiota may drive disease in a genetically susceptible host. Moreover, we show that an individual constituent of the microbiome is sufficient to modulate systemic metabolites through tryptophan metabolism to rewire immunological responses and exacerbate autoimmune disease.



Number of Pages

412 p.

Available for download on Friday, August 04, 2023