Multiple sclerosis (MS) is a neurological disease in which alterations of the gut microbiota can be confirmed by metagenomic analysis. In addition to the 16S rRNA analysis, whole metagenomic analysis, as well as, metabolomic analysis, has been applied in this field, which convincingly proved that the reduction of short chain fatty acids characterizes the intestinal environment of patients with MS. Further research is needed to elucidate the mechanisms responsible for the alterations of the gut microbiome in patients with MS. Characterization of the virome may shed light on.