• The gut-brain axis is attracting much attention in the field of medical science. • Recent research revealed the bidirectional causality between multiple sclerosis (MS) and the gut microbiome. • Microbiome holds the key to understand the mechanisms of onset and progression of MS. • The enhancement of oxidative stress in the gut of MS patients is a promising target of therapy. Recent studies identified specific gut microbial species linked to various human diseases, and gut-brain axis is currently attracting much attention in the field of microbiome science clinically and biologically. Research on multiple sclerosis (MS) and its mouse model, experimental autoimmune encephalomyelitis is one of the most active research subjects. Notably, recent achievements established the bidirectional causality between MS and gut microbiome. The reduction of gut microbiome-derived short chain fatty acids and the enrichment of gut-associated oxidative stress appear to be promoting for neurodegenerative processes. Also, researchers are trying to elucidate the mechanisms by which the microbiome regulates the onset and progression of MS. The new findings achieved by the analysis of the causal relationship between MS and the gut microbiome will provide a new therapeutic strategy for MS. These results will contribute to our understanding of the cause, prevention, and treatment of MS, and will lead to a complete cure for this disease in the future. In MS, for which no curative treatment has yet to be established, the unmet needs may be overcome through the analysis of gut microbiome.