The Gut Microbiome in Multiple Sclerosis Biomarker Signatures, Reproducibility, and Barriers to Translational Therapies

The Gut Microbiome in Multiple Sclerosis

Biomarker Signatures, Reproducibility, and Barriers to Translational Therapies
 

Mimoun Azizi ¹, Dr. Med. Franklin Famdie Simo ², Ibrahim Krenawi *³

1. Chief Physician, Senior Consultant Neurologist and Neurogeriatrician, Klinikverbund Südwest, Sindelfingen, Germany.
2. Senior Consultant Neurologist and Neurogeriatrician, Germany.
3. Consultant Neurologist, Ain Alkhaleej Hospital, Al Ain, UAE.

*Correspondence to: Ibrahim Krenawi, Consultant Neurologist, Ain Alkhaleej Hospital, Al Ain, UAE.

Copyright

© 2026 Ibrahim Krenawi, This is an open access article distributed under the Creative Commons Attribution  License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: 13 July 2026

Published: 01 August 2026

DOI: https://doi.org/10.5281/zenodo.21714969

Abstract

Emerging evidence demonstrates a significant interplay between the gut microbiome and the immunopathogenesis of multiple sclerosis (MS). This review examines the recent evidence on how the presence of the bad types of gut bacteria, disordered metabolism, and other issues can cause brain inflammation. Globally, research invariably concludes that individuals with MS have reduced numbers of bacteria that generate short-chain fatty acids, their metabolism of bile acids is disrupted, and tryptophan-AHR signaling is not firing as it should, all characteristics that make the environment outside the brain more inflammatory. Further experiments indicate that the MS microbiome may indeed cause the central immune system to become more active, which would mean a two-way gut-brain connection. Although the findings are interesting, it is difficult to apply them in actual treatment due to the inconsistencies in the methods, unreliability of such biomarkers, and varied outcomes of the studies. The current methods, such as dietary modifications, probiotics, SCF supplementation, or fecal transplants, merely cause minor immune alterations and have failed to slow the disease. In the future, we should have standardized, specific microbial therapy and longitudinal research that integrates various tools of the omics so that we can develop reliable microbiome-based tools to diagnose and treat MS.

Keywords: Gut Microbiome, Multiple Sclerosis (MS), Neuroinflammation, Short-Chain Fatty Acids (SCFAs), Microbial Dysbiosis, Gut–Brain Axis, Microbiome-Based Therapies.

Abbreviations

Introduction

Multiple sclerosis (MS) has been considered one of the most clinically complicated types of immune-mediated diseases of the central nervous system, which is accompanied by chronic neuroinflammation, demyelination, and progressive neuroaxonal injury. In the past decade, there has been strong evidence of a shift in part of the mechanistic emphasis towards the CNS-intrinsic alone immune dysregulation to the entire immunologic ecosystem that the patient is in. One of these external modulators has become the gut microbiome, which can be biologically credible and clinically relevant, contributing to MS susceptibility, disease activity, and/or therapeutic responsiveness [1], [2].

The gut microbiome is a dynamic immunologic organ that can influence peripheral tolerance, T-cell differentiation, mucosal integrity, and systemic cytokine tone. Its ability to control microglial priming and astrocytic signaling, as well as peripheral effector pathways, has revised the MS pathobiology into a gut-immune-brain axis, with environmental exposures and microbial metabolites communicating directly with neuroimmune networks.

In cohort studies across the world, investigators have found clear-cut taxonomic changes, functional metabolic changes, and immune-modulatory patterns that consistently distinguish MS patients and healthy controls. The basis of these emergent biomarker patterns has been reduced butyrate-producing bacteria, altered mucin-degrading species, disturbed bile-acid transformations, and disrupted tryptophan-AHR-AHR -AHR signaling. Though there is still variability across regions and methodologies, these repeated signals all tend to point to a model that gut dysbiosis is a factor in the systemic inflammatory tone that is seen in MS.

Concurrently, clinical interventional research, such as probiotics, dietary modulation, augmentation of short-chain fatty acids, and fecal microbiota transplantation (FMT), is progressively growing. Although preliminaries indicate immune and metabolic changes, there is still no evidence of conclusive changes on relapse, MRI activity, or disability progression. This is the gap between the potential mechanistic understanding and the dearth of clinical translation, which can explain the urgent need for standardized methodologies, multi-center trials, and harmonized regulatory pathways.

This review aims to achieve three things:

• To generalise existing data on taxonomic, functional, and metabolomic microbiome signatures linked to MS in different populations worldwide.
• To assess the reproducibility and methodological heterogeneity, it is necessary to define the most trustworthy biomarkers and explain why the findings were not consistent.
• To evaluate critically translational barriers such as regulatory, safety, methodological, and data-standardization barriers, which, as presently exist, have impeded the entry of microbiome-based diagnostics or therapeutics into routine MS care.

This systematic review combines human cohort studies, cross-sectional and longitudinal microbiome studies, mechanistic animal studies, interventional clinical trials, and methodological commentaries. We are interested in clinically meaningful interpretation, which is the translation of complicated microbiome science into practiceable insights to physicians, without disregarding the limitations and the unmet needs as emphasized throughout the literature.

Methods and Evidence Acquisition Strategy

In order to create a clinically significant synthesis of gut microbiome research in multiple sclerosis (MS), we performed a multi-level literature analysis encompassing traditional taxonomic research as well as new functional, metabolic, and translational research [16]. The method is similar to the rigorous methodology of the initial, focusing on the generality of evidence, transparency of the methodology, and clinical applicability (Methodology and standardization commentaries, 2024–2025).

Literature Search Strategy

Systematic searches were performed across PubMed/PMC, EMBASE, Web of Science, Scopus, ClinicalTrials.gov, and major biomedical publishers (Nature, Cell, PNAS), using combined terms such as “multiple sclerosis,” “gut microbiome,” “gut microbiota,” “metagenomics,” “16S rRNA,” “shotgun metagenomics,” “metabolomics,” “short-chain fatty acids,” “probiotics,” and “fecal microbiota transplantation.”

To make the medical content relevant to the real world, further authoritative web-based clinical sources were consulted, such as the Cleveland Clinic, NIH, and the National Multiple Sclerosis Society, which consistently release clinical overviews on the effect of the microbiome on systemic immune regulation. As an example, in 2024, the NIH reported that gut microbial dysbiosis might lead to extra-CNS immune activation in MS, and the role of microbial metabolites in translation is therefore of critical interest [4].

Inclusion and Exclusion Criteria

The inclusion criteria were similar to yours and concentrated on:

• The human MS research evaluated the gut microbial composition or metabolic products through 16S sequencing, shotgun metagenomics, or metabolomics [1].
• Probiotics, prebiotics, dietary modification, SCFA supplementation, or FMT [5].
• Mechanistic experiments, where human-derived microbiota are applied in the induction or prevention of neuroinflammation in murine models.

The exclusion criteria removed those studies in which the methodology, the metadata, or anecdotal statements about the microbiome were not validated by sequencing.

Data Extraction and Synthesis Approach

In each of the studies, we have extracted cohort characteristics, sampling and sequencing procedures, taxonomic and functional findings, metabolomic signatures, and immune correlations [5], [6].

In light of the high level of heterogeneity of the sampling practices, sequencing platforms, and bioinformatics pipelines, a quantitative meta-analysis was intentionally foregone [7]. Rather, a qualitative synthesis was used, with bias towards findings that could be replicated in independent cohorts, diverse technologies in sequencing, and different geographies.

Global Gut Microbiome Signatures in Multiple Sclerosis

A reproducible (albeit subtle) trend of gut microbial dysbiosis in MS has been set over the last ten years. Although there is no absolute uniformity between studies, there are a number of taxonomic signatures that are repeated often enough to be deemed clinically significant [1].

Recurrent Taxonomic Alterations Across Cohorts

Among geographically dispersed cohorts, the decline of butyrate-producing Firmicutes with the leading role in Faecalibacterium prausnitzii, an important anti-inflammatory commensal, and a well-known participant in Tregs induction and intestinal barrier stabilization, is one of the most recurring [1]. This is one of the most biologically feasible and the most powerful microbiome signatures in MS [5].

Moreover, several studies have described changes in mucin-degrading species, specifically, Akkermansia muciniphila [6]. Despite the inconsistent findings in different cohorts, greater Akkermansia abundance seems in numerous MS datasets and could lead to dysregulated mucosal-immune interactions.

Similarly, Prevotella has variable yet noteworthy changes that have been described. Some cohorts have the characteristic depletion of Prevotella species - inflammatory metabolite-associated microbes, although the replication across areas is inconsistent [8].

Enrichment of Potentially Pro-Inflammatory Taxa

Intermittent Desulfovibrio enrichment, discrete Clostridium clusters, and Methanobrevibacter can be found in MS microbiomes, associated in some settings with mucosal inflammation and perturbed epithelial signaling [9]. These findings may not be universal but are part of a larger trend indicating an immunostimulatory change in gut ecology.

Integration of External Clinical Data

The clinical institutions have also become more aware of the significance of these alterations in microbes.

• In 2023, the Cleveland Clinic described that the decreased state of butyrate-producing organisms, such as Faecalibacterium and Eubacterium, can weaken mucosal immune tolerance and lead to low-grade systemic inflammation in MSs.
• In 2024, the NIH reported that mucin-degrading species, especially Akkermansia, which have been altered, can contribute to disease activity through heightened intestinal permeability and altered peripheral cytokine tone [4].
• The National MS Society has pointed out that patients with lower Prevotella content might not have as favorable metabolic and immune signatures.

These clinical findings are in complete agreement with the different studies mentioned that support their translational applicability.

Cross-study Consistency and Limitations

Nevertheless, in the recurrent patterns, it rightfully points out that effect sizes are not large and cohort heterogeneity is still considerable, in large part owing to geographical factors, eating behaviors, exposure to medication, and varying sequencing techniques [3]. Further multicenter investigations and robust longitudinal constructs are required to reveal the possibility of such microbial signatures acting as a viable clinical biomarker.

Functional and Metabolomic Biomarker Profiles in Multiple Sclerosis

Some of the most interesting evidence supporting the association between intestinal dysbiosis and multiple sclerosis (MS), however, involves the functional activity of the gut microbiome, its metabolites, enzymatic processes, and immune-modulatory secretions. Both functional and metabolic patterns are far more consistently cross-study reproducible than taxonomic profiles, and thus microbial metabolites play a central role in determining systemic and CNS immunobiology, [1], [5].

Three metabolic domains are recurrently found in global MS cohorts, including short-chain fatty acids (SCFAs), bile-acid derivatives, and tryptophan AHR pathways. The pathways are not only quantifiable but also biologically realistic biomarkers that directly regulate the immune tone, intestinal integrity, and neuroinflammatory signaling.

Short-Chain Fatty Acids (SCFAs): Central Immunometabolic Regulators

One of the most reproducible findings in MS-related microbiome studies, is the reduced levels of SCFA and especially of butyrate and propionate [10]. SCFAs are strong epigenetic and immunoregulatory metabolites that enhance differentiation of regulatory T-cells (Treg) to stabilize epithelial barrier activity and tone down pro-inflammatory cytokine transmission [1].

The numerous MS cohorts, time and again, show:

• Loss of butyrate-producing commensals, including Faecalibacterium prausnitzii and Lachnospiraceae [5].
• Lower fecal and serum concentrations of SCFA, which are associated with the lower values of the peripheral Treg frequency [8].

External clinical context

In 2023, the Cleveland Clinic reported that the low level of SCFA could weaken mucosal tolerance, increase intestinal permeability, and enhance systemic immune activation, an axis that has been identified as an increasing part of MS clinical pathophysiology [11], [17]. Likewise, in 2024, the NIH underlined the potential of SCFAs as biomarkers of immune homeostasis in autoimmune diseases due to their ability to regulate microglial and astrocyte signaling.

Bile Acids and Microbial Steroid Metabolism

MS cohorts often exhibit disturbed bile-acid pools and disturbed microbial conversion of primary to secondary bile acids metabolic pathways capable of activating bile acid receptors, including FXR and TGR5, both of which have immunoregulatory activity in the CNS [5].

Several translational research studies indicate that bile-acid derivatives may exert their effect on:

• Microglial polarization
• Astrocyte inflammatory profiles
• Peripheral T-cell differentiation [6]

External clinical context

According to the National MS Society, the literature on the subject indicates that recent studies indicate that bile-acid metabolites can influence neuroinflammatory pathways through the regulation of glial reactivity and systemic cytokine tone.

Tryptophan Metabolism and AHR Signaling

Microbial products of tryptophan, specifically ones based on indols, activate the aryl hydrocarbon receptor (AHR), an immune and neuroimmune regulatory center involved in the development of MS. Here is notable emphasis on the fact that MS cohorts tend to be disrupted in this metabolic axis, which is down-regulated in microglial homeostasis and T-cell effector T-cell action [9].

These changes indicate that tryptophan-microbiota interaction can be used as a dynamic biomarker of immune dysregulation.

External clinical context

In 2024, the Mayo Clinic observed that AHR-stimulating metabolites affect CNS immune patrol and glial stimulation, and this pathway was noted as a potential interface to understand the gut-brain immunologic axis of neuroinflammatory illnesses.

Integrated Multi-omic Biomarker Panels

Joint metabolic signatures- as opposed to mono microbial taxa- provide the greatest reproducibility between independent cohorts [18]. Multi-omic panels that include:

• SCFAs,
• bile-acid derivatives,
• tryptophan metabolites,
• and associated immune markers

show much more cross-study stability and diagnostic capabilities than taxonomic profiling [6].

External clinical context

Various clinical facilities, such as the Cleveland Clinic and NIH, have now underscored the fact that functionally defined biomarkers such as SCFA signatures and bile-acid profiles may be used in the future as indicators of MS activity in therapeutic responsiveness or risk stratification.

The best biomarkers of gut dysbiosis predicting MS pathophysiology are functional and metabolomic signatures, including SCFA depletion, disturbed bile-acid conversion, and tryptophanAHR signaling dysregulation, which form the strongest, biologically coherent signals of gut dysbiosis [19], [17]. These o