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Updated: Jun 28, 2026
Simultaneous Isolation of Principal Central Nervous System-Resident Cell Types from Adult Autoimmune Encephalomyelitis Mice
Published on: October 6, 2023
Integrated multi-omics analysis identifies microbial and metabolic signatures and drivers of CNS autoimmunity
Theresa L Montgomery1, Emily A Nelson1, Lauren A Downs1
1Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05401, USA.
Abstract:
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) driven by genetic and environmental determinants. The gut microbiome of people with MS (pwMS) is distinct and influences disease through immunomodulatory metabolite production. Circulating metabolites are altered in pwMS, but identifying microbial-metabolic drivers remains challenging. We previously showed that colonization by the gut commensal Limosilactobacillus reuteri (L. reuteri) exacerbates disease in the experimental autoimmune encephalomyelitis (EAE) model of MS, in a tryptophan-dependent manner. Here, we integrated microbiomic and metabolomic datasets from a longitudinal EAE study utilizing high and low tryptophan diets in mice colonized or not with L. reuteri. Gut microbiome dynamics under short- and long-term alterations in tryptophan bioavailability, were affected by diet, microbiome context, or disease. During short-term dietary intervention, L. reuteri colonization exerted a greater impact on microbiome composition than tryptophan bioavailability. With longer dietary exposure and EAE progression, high dietary tryptophan and L. reuteri colonization synergized to elicit profound microbiota changes, including alterations in Lachnospiraceae, Blautia, and Akkermansia. Integration of metabolomic and microbiomic datasets using joint Robust Aitchison PCA revealed clusters of associated metabolites and microbiota enriched for functional pathways, including bile acid and tryptophan metabolism. Metabolites outperformed microbiota in predicting EAE severity, identifying p-cresols and indoles as top disease-associated metabolites. Treatment with p-cresol or 3-indoleglyoxylic acid exacerbated EAE, enhanced proinflammatory T cell responses, and increased cerebellar pathology. These data demonstrate that dietary responses are shaped by gut microbiome composition and that integrated microbiomic-metabolomic analyses can identify drivers of disease worsening in MS.
Insights
Diet and gut microbes interact to influence multiple sclerosis (MS) severity. Specific metabolites produced by gut bacteria can worsen MS disease, suggesting new therapeutic targets.
Area of Science:
- Neuroimmunology
- Microbiome Research
- Metabolomics
Background:
- Multiple sclerosis (MS) is an autoimmune central nervous system (CNS) disease influenced by genetic and environmental factors.
- The gut microbiome composition and its produced metabolites are distinct in people with MS (pwMS) and impact disease.
- Identifying specific microbial-metabolic drivers of MS exacerbation remains challenging.
Purpose of the Study:
- To investigate how diet and gut microbiota interactions influence immunomodulatory metabolites in a mouse model of MS.
- To identify specific microbial metabolites that can exacerbate MS disease.
- To assess the utility of integrated microbiome-metabolome analysis for predicting MS disease severity.
Main Methods:
- Longitudinal experimental autoimmune encephalomyelitis (EAE) study in mice with varying tryptophan diets and Limosilactobacillus reuteri colonization.
- Integrated analysis of gut microbiome and serum metabolomic datasets using joint Robust Aitchison PCA.
- Predictive modeling to correlate metabolites and microbiota with EAE severity; validation by treating mice with identified metabolites.
Main Results:
- High dietary tryptophan and L. reuteri colonization synergistically altered microbiota composition, including Lachnospiraceae, Blautia, and Akkermansia.
- Metabolites, particularly p-cresols and indoles, were better predictors of EAE severity than microbiota composition.
- Treatment with p-cresol or 3-indoleglyoxylic acid exacerbated EAE, increased pro-inflammatory T cell responses, and worsened cerebellar pathology.
Conclusions:
- Dietary responses are significantly shaped by gut microbiome composition.
- Integrated microbiomic-metabolomic analyses effectively identify microbial metabolites that drive MS disease worsening.
- Targeting microbial metabolites or diet-microbiome interactions presents potential therapeutic strategies for MS and related autoimmune disorders.
