By Joseph E. Scherger, MD, MPH

Vice President, Primary Care, Eisenhower Medical Center; Clinical Professor, Keck School of Medicine, University of Southern California

Dr. Scherger reports no financial relationships relevant to this field of study.

SYNOPSIS: Increasing evidence suggests that dysbiosis, a disorder in the gut microbiome, leads to autoimmune diseases, including multiple sclerosis.

SOURCE: Glenn JD, Mowry EM. Emerging concepts on the gut microbiome and multiple sclerosis. J Interferon Cytokine Res 2016;36:347-357.

Two scientists from the Department of Neurology at Johns Hopkins University School of Medicine recently reviewed the emerging science of the human gut microbiome and the development of autoimmune diseases, particularly multiple sclerosis. The gut microbiome has complex bidirectional interactions with the human immune system.

While the bacteria in the human gut has the highest density ever recorded in any ecosystem, there are even more viruses in the gut, most importantly the bacteriophages that infect the bacteria and exchange DNA.

The microbiome develops at birth and is enhanced by both vaginal delivery and breastfeeding. Children born by C-section have a delay in their microbiome development as do children not breast fed. These changes have been reported for up to seven years. Multiple sclerosis patients feature a higher rate of C-section birth and shorter duration of breastfeeding than controls.1,2

There is emerging evidence leading researchers to believe that dysbiosis, disorders in the gut microbiome, form a biological basis for the development of autoimmune diseases. Some of the strongest evidence exists for Crohn’s disease and multiple sclerosis.3,4 The Western diet, with its unhealthy trans fats, excessive sugar, and inflammatory proteins, has been associated with dysbiosis.


The number of books written by physicians and biologists on the gut microbiome has exploded in the last few years.5-8 Compelling evidence says our health depends on what we eat in profound ways, with the gut microbiome acting as a critical intermediary. Disorder in the gut microbiome has become the leading theory behind the development of autoimmune diseases.

Terry Wahls is an internist at the University of Iowa who developed disabling multiple sclerosis in 2002. Conventional therapy, including new biologic agents, were ineffective in halting the progression of her disease. After years of research into scientific articles, she adopted an anti-inflammatory diet that over time halted and then reversed her disease, and she is now fully functional. She runs an ongoing clinical trial at the University of Iowa and has helped hundreds of other multiple sclerosis patients. Her 2014 book, The Wahls Protocol, describes her therapeutic approach in detail.9

The human microbiome exists throughout the body, with 70% of the organisms residing in our gut. Research into its many functions in health and disease are early in their development. It is likely that an understanding of the interactions and effects of the microbiome on our bodies will profoundly change medical practice in the years to come.


  1. Neu J, Rushing J. Cesarean versus vaginal delivery: Long-term infant outcomes and the hygiene hypothesis. Clin Perinatol 2011;38:321-331.
  2. Pisacane A, Impagliazzo N, Russo M, et al. Breastfeeding and multiple sclerosis. J Leukoc Biol 1994;308:1411-1412.
  3. Lepage P, Colombet J, Marteau P, et al. Dysbiosis in inflammatory bowel disease: A role for bacteriophages? Gut 2008;57:424-425.
  4. Cantarel BL, Waubant E, Chehoud C, et al. Gut microbiota in multiple sclerosis: Possible influence of immunomodulators. J Investig Med 2015;63:729-734.
  5. Permutter D. Brain Maker. New York: Little, Brown and Co.; 2015.
  6. Chutkin R. The Microbiome Solution. New York: Avery (Penguin Group); 2015.
  7. Sonnenburg J, Sonnenburg E. The Good Gut. New York: Penguin Press; 2015.
  8. Mullen G. The Gut Balance Revolution. New York: Rodale; 2015.
  9. Wahls T. The Wahls Protocol. New York: Avery (Penguin Group); 2014.