People with MS consistently show altered gut microbiome composition, including the loss of microbial taxa associated with immune regulation and the enrichment of taxa associated with inflammatory signaling.
In an early human cohort, gut microbial profiling of RRMS patients revealed distinct communities compared with healthy controls, with increased abundance of genera such as Pseudomonas, Mycoplana, Haemophilus, Blautia, Dorea and decreased abundance of Parabacteroides, Adlercreutzia, Prevotella.
Subsequent work demonstrated that not only the bacterial microbiota but also the gut mycobiome differ in MS: RRMS patients had an elevated fungal‐to‐bacterial richness ratio, altered fungal genera (e.g., increased Candida, Epicoccum; decreased Saccharomyces) and disrupted fungal, bacterial network associations.
In our most recent study, using shotgun metagenomic sequencing in a large international cohort, we identified a specific microbial ratio, lower Bifidobacterium adolescentis: Akkermansia muciniphila (BA:AM), as a hallmark of MS patients, which also correlated with disease severity in preclinical EAE models.
Key Findings & Interpretation
- MS is associated with reproducible gut dysbiosis, including loss of potentially beneficial microbes (e.g., Prevotella) and enrichment of inflammation-associated taxa.
- The gut mycobiome is also altered, highlighting the importance of considering the full microbial ecosystem (bacteria + fungi).
- The BA:AM microbial ratio serves as a potential microbial signature of MS and correlates with disease activity.
- Mechanistically, these microbial shifts are not merely correlational—they can predispose to or exacerbate neuroinflammation in experimental models.
Future Directions
We are now pursuing:
- Longitudinal tracking of gut microbiome/metabolome signatures in MS patients over time, to assess whether specific changes precede disease flares or progression.
- Functional studies of microbial metabolites (and microbial–host metabolite axes) to identify mechanistic pathways by which microbes influence immune regulation and CNS inflammation.
- Translation of findings into microbiome‐based diagnostic tools, and development of microbiome‐informed therapeutic strategies (e.g., precision nutrition, microbial supplementation/engineering) aimed at restoring immune balance in MS.
Selected Publications
Ghimire S, Lehman P, Shahi SK, et al. “Specific microbial ratio in the gut microbiome is associated with multiple sclerosis.” Proc Natl Acad Sci USA. 2025;122(10):e2413953122. PMID:40030030
Yadav M, Ali S, Shrode RL, et al. “Multiple sclerosis patients have an altered gut mycobiome and increased fungal to bacterial richness.” PLoS One. 2022;17(4):e0264556. PMID:35472144
Chen J, Chia N, Kalari KR, Yao J, Novotna M, et al. “Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls.” Sci Rep. 2016;6:28484. PMID:27346372