Humans serve as a major reservoir for a vast number of microbiota. These microbes have evolved symbiotic relationships with humans due to their close proximity with their host. As a result, the immune system adapts to the microbiota thus modulating immunological function. Autoimmunity is a state in which there are aberrant immune responses produced against host tissue. Intestinal bacteria are directly impacted by instances of inflammation brought on by autoimmunity. The complicated nature between autoimmunity and bacterial modulation demonstrates a bi-directional relationship. Here, we utilize experimental autoimmune encephalomyelitis, a model for multiple sclerosis, to explore the bi-directional relationship that disease and microbiota share. We demonstrate that disease severity, as well as time point post disease induction, shapes the structure and function of the gut microbiome. Additionally, antibiotic intervention modulates the symptoms of disease by upregulating the expression of T regulatory cells. Further, we show that a genetically engineered Lactococcus lactis expressing the colonization factor antigen I from Escherichia coli acting as an immunomodulatory probiotic reduced the severity of disease.