Longitudinal Stability of the Gut Microbiota in Relapsing–Remitting Multiple Sclerosis: A Prospective Observational Study

The gut microbiota plays a key role in immune regulation in multiple sclerosis (MS), yet longitudinal data on microbiome dynamics and their relationships with disability and biomarkers remain limited. This study aimed to identify longitudinal gut microbiome changes in patients with relapsing-remitting multiple sclerosis (RRMS) and their association with disability and specific serum biomarkers, including predicted metabolic pathways. In this prospective longitudinal study, 29 treatment-naïve RRMS patients were evaluated at baseline and after one year of disease-modifying therapy. Clinical assessments included the Expanded Disability Status Scale (EDSS) and disability tests. Serum glial fibrillary acidic protein (GFAP), neurofilament light chain (NfL), and S100B protein concentrations were measured at both visits. Gut microbiota composition was characterized by shotgun metagenomic sequencing, including taxonomic composition, diversity measures, functional pathways, gut metabolic modules, and gut–brain modules. In the 29 patients, overall gut microbiota composition and diversity remained stable during follow-up. Although EDSS progression was associated with a trend toward greater microbiome instability, this association did not reach statistical significance. Several bacterial taxa and predicted metabolic pathways showed nominal associations with disability, but were not significant after correction. GFAP levels increased significantly over time, whereas NfL levels decreased and S100B levels remained unchanged. Early RRMS is characterized by a stable gut microbiome during the first year of treatment. Exploratory taxonomic and functional associations did not remain significant after correction for multiple testing, highlighting the need for larger longitudinal cohorts.