Innovations in the Treatment of Autoimmune Diseases

The frequency of autoimmune disease throughout Westernized societies has increased significantly over the last 30 years,1 causing chronic, debilitating dysfunction in those who suffer from these diseases. While much of the conventional treatment for autoimmune disease is aimed at relieving the pain or symptoms through immune-suppressing medications, Functional Medicine offers an alternative to symptom suppression—by addressing the underlying mechanisms that cause autoimmunity, we can prevent, and in some cases reverse autoimmune diseases.

Elizabeth Boham, MD, MS, RD, is board certified in family medicine and has a strong background in nutrition and Functional Medicine.

At IFM’s 2018 Annual International Conference (AIC), Solving the Puzzle of Autoimmunity: The Interplay of Gut, Genes, and Environment, practitioners learned about a variety of innovative treatment options that optimize outcomes for autoimmune disease patients. Functional Medicine practitioners have long recognized that dysregulation of tight junctions, or intestinal permeability, can play a critical role in the development of autoimmune disease.2 Imbalances in the gut, such as dysbiosis, can interfere with tight junctions, allowing antigenic food particles, toxic agents, microorganisms, and bacterial byproducts to cross the gut lumen and induce an immune response that can culminate in autoimmunity.2

Restoring equilibrium in the gut microbiota, which can in turn promote repair of the mucosal barrier, is a key strategy for arresting autoimmunity. When food and lifestyle aren’t enough, a fecal microbiota transplant (FMT), covered at AIC in a session by Mark Davis, ND, is another option for healing the gut. FMT involves the transfer of the fecal microbiota from a healthy donor to a diseased recipient in order to restore a balanced gut microbial ecology.3

Studies show that this innovative treatment restores depleted bacteria, which in turn promote immunomodulatory effects.4 For patients with irritable bowel disease, meta-analysis demonstrated that 45% of subjects achieved clinical remission with FMT.5 Another study concluded that FMT has a 34.1% cure rate and 68.2% improvement rate for ulcerative colitis and a 30.0% cure rate and 60.0% improvement rate for Crohn’s.6 FMT has also emerged as an effective and safe therapy for recurrent C. difficile infection, with a success rate of over 80%.7

Natural immunomodulators can also be used in the treatment of autoimmune disease, as Eric Yarnell, ND, RH(AHG), discussed at the 2018 AIC. Herbs that reduce inflammation may help downregulate the autoimmune response and include hops, artemisia, sarsaparilla, reishi mushroom, ashwagandha, nettle, rehmannia, and Chinese skullcap.8

Other treatment options for autoimmune disease patients that were covered at IFM’s AIC included:

  • “Low-Dose Naltrexone and Autoimmune Disease,” presented by Jill Cottel, MD, and Leonard Weinstock, MD
  • “Helminth Therapy in Autoimmune Disease,” presented by William Parker, PhD, and Sidney Baker, MD
  • “An Integrative Approach to the Treatment of Inflammatory Bowel Disease,” presented by Gerry Mullin, MD
  • “Using a Systems-Based Approach in the Management of RA and SLE,” presented by George Munoz, MD
  • And many more…

View the Conference Proceedings to explore clinical topics from IFM’s 2018 Annual International Conference on autoimmunity.


Learn More about IFM’s Annual International Conference


  1. Lerner A, Jeremias P, Matthias T. The world incidence and prevalence of autoimmune disease is increasing. Int J Celiac Dis. 2015;3(4):151-155. doi:10.12691/ijcd-3-4-8.
  2. Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol. 2012;42(1):71-78. doi:10.1007/s12016-011-8291-x.
  3. Cammarota G, Ianiro G, Gasbarrini A. Fecal microbiota transplantation for the treatment of Clostridium difficile infection: a systematic review. J Clin Gastroenterol. 2014;48(8):693-702. doi:10.7326/M14-2693.
  4. Xu M, Cao H, Wang W, et al. Fecal microbiota transplantation broadening its application beyond intestinal disorders. World J Gastroenterol. 2015;21(1):102-111. doi:10.3748/wjg.v21.i1.102.
  5. Colman R, Rubin D. Fecal microbiota transplantation as therapy for inflammatory bowel disease: a systematic review and meta-analysis. J Crohns Colitis. 2014;8(12):1569-1581. doi:10.1016/j.crohns.2014.08.006.
  6. Li N, Tian H, Ma C, et al. Efficacy analysis of fecal microbiota transplantation in the treatment of 406 cases with gastrointestinal disorders. Zhonghua Wei Chang Wai Ke Za Zhi. 2017;20(1):40-46.
  7. Millan B, Park H, Hotte N, et al. Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection. Clin Infect Dis. 2016;62(12):1479-1486. doi:10.1093/cid/ciw185.
  8. Zampieron ER, Kamhi EJ. Natural support for autoimmune and inflammatory disease. J Restorative Med. 2012;1(1):38-47.
  9. Lerman RH, Chang JL, Konda V, Desai A, Montalto MB. Nutritional approach for the relief of joint discomfort: a 12-week, open-case series and illustrative case report. Integr Med. 2015;14(5):52-61.
  10. Desai A, Darland G, Bland JS, Tripp ML, Konda VR. META060 attenuates TNF-alpha-activated inflammation, endothelial-monocyte interactions, and matrix metalloproteinase-9 expression, and inhibits NF-kappaB and AP-1 in THP-1 monocytes. Atherosclerosis. 2012;223(1):130-136. doi:10.1016/j.atherosclerosis.2012.05.004.
  11. Tripp M, Darland G, Lerman R, Lukaczer D, Bland J, Babish J. Hop and modified hop extracts have potent in vitro anti-inflammatory properties. Acta Hortic. 2005;668:217-228. doi:10.17660/ActaHortic.2005.668.28.
  12. Kumar G, Srivastava A, Sharma SK, Rao TD, Gupta YK. Efficacy & safety evaluation of Ayurvedic treatment (Ashwagandha powder & Sidh Makardhwaj) in rheumatoid arthritis patients: a pilot prospective study. Indian J Med Res. 2015;141(1):100-106.

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