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The Microbiome and Autoimmune Disease

By Elaine Moore on 12/15/2016

Since the 1990s autoimmune diseases have been known to develop in genetically predisposed individuals when exposed to certain environmental triggers, including infectious agents, allergens, various chemicals and stress. Theories describing how autoimmune diseases develop include molecular mimicry, a condition where microbes change their appearance to mimic the body's proteins which leads to an attack on these proteins and the production of autoantibodies; and leaky gut syndrome, a condition in which the permeability of the gut is impaired, causing microbes and food proteins to leak into the blood stream.

The human microbiome represents the microbes that persist in an individual's body. Typically, humans harbor 10 times as many microbes as human cells. The gut microbiome refers to the microbes within the intestines. Microbes are essential for life. In good health the body's normal microbial flora remain balanced and assists in digestion as well as the production of vitamins and other chemicals.

In autoimmune diseases, the microbiome differs from the microbiome found in those without autoimmune diseases and remains in a state of imbalance known as dysbiosis. Because microbes can regulate gene function, this dysregulation can lead to changes in immune system cells that contribute to autoimmune disease development. Microbes have been known to alter the expression of human genes and in particular that of the vitamin D nuclear receptor (VDR), which explains the low levels of 25 OH vitamin D seen in patients with autoimmune disease. The Epstein-Barr virus (EBV) slows expression of the VDR in immature lymphoblastoid (lymphocyte cell precursors) cell lines by a factor of greater than thirty. Borrelia burgdrferi, cytomegalovirus and Mycobacterium species also decrease receptor activity to varying degrees.

There are millions of genes in microbes (bacteria, fungi, viruses) compared to the 20,500 genes present in the human genome. Proal and her colleagues explain how microbes such as Lactobacillus and Bifidobacteria, which are present in dairy products, can downregulate expression of human angiotensin regulating enzyme (ACE) acting like ACE inhibitors to lower blood pressure. However, when certain microbes predominate, they too are associated with disease development. For instance, EBV is associated with a number of autoimmune disorders including multiple sclerosis, Graves' disease, and Sjogren's disease.  Reactive arthritis can develop after infections with Salmonella, Shigella and Yersinia and Proteus infection is known to trigger rheumatoid arthritis.

What This Means

The microbiome is passed down from mother to child with some researchers stating that the microbiome has more of an effect on our health than our genes do. This certainly seems to be the case in autoimmune disease where 20% of the population has genes that predispose them to autoimmune disorders but less than 7% of the population develop these disorders.  One's microbiome can be imbalanced by a number of different factors including chronic infections, overuse of antibiotics, various chemicals and chemical adjuvants found in some vaccines, allergens, hybridized grains, foods contaminated with hormones and pesticides, artificial sweeteners, excess sugar, C-sections, and others. Besides its effects on autoimmune disease development, the microbiome can affect how much fat we store, and it can cause bouts of depression. The microbiome can be healed or restored over time with diet, especially the avoidance of allergens, hybridized grains and sugar, and by adding prebiotics and probiotics to a diet rich in organic and grass-fed foods.

A study using data from the The Environmental Determinants of the Diabetes in the Young (TEDDY) study group demonstrated that gluten consumption during late pregnancy causes an increased risk of celiac disease in offspring. While there are numerous studies showing a link between infectious agents and autoimmune diseases, other studies have demonstrated the effectiveness of simple changes such as swabbing newborns born by C-section with vaginal swabs from their mothers to provide a normal microbiome for the neonate. Other studies have shown how kefir and Kombachu can help restore the microbiome. Studies have even shown that fecal transplants to change bacterial flora can also induce improvement in certain autoimmune conditions.

A novel theory for treating autoimmune diseases has been proposed by Proal and her team. These researchers explain that suppression of the immune system, the traditional treatment for systemic and connective tissue autoimmune diseases, gives a temporary relief from symptoms but not a long term cure. Because the immune system in autoimmune disease is weak, they propose that treatment designed to stimulate the immune system would allow it to initiate its own healing process. By producing more cytokines and chemokines, the immune response would indeed be more vigilant. While immune stimulants such as echinacea and vaccines have been known to exacerbate symptoms of autoimmune diseases, remedies such as immunomodulators that strengthen the immune system offer great promise.


Uusitalo U, Lee H, Aronsson D, Yang J, Virtanen S, Norris J, and D Agardh for the TEDDY study group. 2015. "Gluten consumption during late pregnancy and risk of celiac disease in the offspring." American Journal of Clinical Nutrition, Oct 7.

 Proal D, Albert PJ, and TG Marshall. 2013. "The human microbiome and autoimmunity." Current Opinions in Rheumatology. Mar; 25(2):234-40.



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