The gut microbiome plays a crucial role in immune function and has been implicated in various autoimmune disorders, including multiple sclerosis (MS). This study investigates the gut microbiome in MS patients (n=60) and healthy controls (n=43) using 16S rRNA sequencing. Key findings include increased *Methanobrevibacter* and *Akkermansia* and decreased *Butyricimonas* in MS patients, which correlate with variations in genes involved in dendritic cell maturation, interferon signaling, and NF-kB signaling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased *Prevotella* and *Sutterella* and decreased *Sarcina*. A second cohort of MS patients showed elevated breath methane, consistent with increased *Methanobrevibacter* in the gut. These alterations suggest that the gut microbiome may play a role in MS pathogenesis, potentially through immune modulation. Further research is needed to determine whether these microbial changes are a cause or consequence of MS.The gut microbiome plays a crucial role in immune function and has been implicated in various autoimmune disorders, including multiple sclerosis (MS). This study investigates the gut microbiome in MS patients (n=60) and healthy controls (n=43) using 16S rRNA sequencing. Key findings include increased *Methanobrevibacter* and *Akkermansia* and decreased *Butyricimonas* in MS patients, which correlate with variations in genes involved in dendritic cell maturation, interferon signaling, and NF-kB signaling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased *Prevotella* and *Sutterella* and decreased *Sarcina*. A second cohort of MS patients showed elevated breath methane, consistent with increased *Methanobrevibacter* in the gut. These alterations suggest that the gut microbiome may play a role in MS pathogenesis, potentially through immune modulation. Further research is needed to determine whether these microbial changes are a cause or consequence of MS.