The recognition of the “multiple sclerosis microbiome” is an exciting and emerging addition to the research surrounding the condition. Although there is great promise and much hope that the microbiome will provide an opportunity to enhance our understanding of what causes multiple sclerosis and drives the disease process(es), much remains unknown. Animal models of multiple sclerosis provided the first intriguing evidence of the potential for the microbiome to play a substantial role as either a precipitating factor in triggering multiple sclerosis onset or as a facilitator of subsequent disease activity. Animal studies have included lung tissue samples to assess the microbiome, as lung tissue may be an important site of immune activation. The role of antibiotics or phage treatment remains other theoretical possibilities to alter the gut microbiome in multiple sclerosis. The focus naturally is on humans—multiple sclerosis is thought to only affect Homo sapiens—and on the gut microbiome.