The Microbiome: An Essential Treatment for Healing Autoimmune Disease

I see a lot of patients struggling with different types of autoimmune conditions. Many come in with questions about how to eat and the elimination diets that are so popular right now. Often they’ve tried several only to wind up in my office feeling terrible and unsure of what to do next. One reason may be due to the disproportionately large amounts of meat that some elimination diets include. Another may have to do with the health of their gut bacteria.

Its trendy for people with autoimmune disease to try eating Paleo or take it step further to its stricter sister diet AIP- Autoimmune protocol. Followers of AIP remain on a modified Paleo diet indefinitely avoiding specific foods they are sensitive to as well as all grains, quinoa, potatoes, legumes, processed sugars, salt, dairy, nuts and seeds. That’s pretty restrictive. So what’s left to eat? Lots of meat with some fruit and vegetables. In fact many Paleo “experts” recommend as much as 55% of calories come from meat in the name of reversing inflammation. We will look at these diets in a moment.

Autoimmune disease actually refers to over 80 health conditions that develop though an over-activity or misfiring of the immune system. As many as 23 million people are affected right now in the USA alone-78% of them women. Our bodies have the amazing ability to create antibodies to protect us. They are the tiny soldiers that wage war on foreign invaders, unfriendly bacteria and viruses that would otherwise be unstoppable. But what happens when something goes wrong? Food triggers, inflammation and shifts in the microbiome can spark the production of antibodies against our own healthy tissues. The immune system may even loose the ability to shut down after an attack damaging organs, cells and anything in its path. The destruction can be catastrophic and target almost anyplace in the body if conditions are right.

Why are autoimmune diseases on the rise?

Genetics, stressors and environmental toxins are all contributing factors but the answer is also found at the end of our forks. What we eat has a direct impact on the type of bacteria that dominate the gut flora of the microbiome. The microbiome is the community of different species that make up the trillions of bacteria in our bodies, largely throughout our digestive tract. We are actually 10 times more bacterial cells than human cells! When its healthy, the microbiome will be stable, diverse and populated with “friendly” bacteria that support us. When this balance is disturbed, a variety of conditions can result including autoimmune disease. It makes sense since most of our immune system is located in the gut. Research in this area is exploding as it becomes more apparent that our health and function may actually be a reflection of the health and well being of the microbiome!

Happy families are similar.

Several recent studies compared the glut flora of children with Type 1 Diabetes to control groups of healthy kids. T1D is an autoimmune disease of the pancreas that attacks and destroys the insulin producing cells. Without insulin the body is unable to process and use sugar to make energy.

A diverse, friendly microbiome works synergistically to protect us against autoimmunity.

The results? Healthy children had much higher concentrations of friendly bacteria that support intestinal health by producing butyrate- a fuel for the cells of the large intestine (1). They also had a more stable and diverse microbiome that was similar from person to person (2) (3). The T1D groups had less diverse and beneficial bacteria in a less stable gut environment that varied more from person to person(1). Researchers summed it up with this quote from Tolstoy’s Anna Karenina: “All happy families are alike; each unhappy family is unhappy in its own way (2).” I’ll sum it up by saying a diverse, friendly microbiome works synergistically to protect us against autoimmunity.

Its not rocket science (its just common sense and good food!)

Our relationship is symbiotic. Gut bacteria need us as a host to live. In return they actually have the power to interact with our immune system and help protect us from its potentially dangerous malfunctions. I’m speaking about the helpful species that flourish and dominate when they receive the proper nutrients. Of course not all bacteria are created equal. Harmful bacteria love processed junk foods like those found in the Standard American Diet. Packaged food loaded with refined sugar, flour, additives, chemicals, harmful fats and a lack of fiber will make them very happy. Studies show even too much meat like the 55% recommended by the Paleo movement can be inflammatory, is linked to cancer and can shift the type of bacteria that are present impacting our health.

Lets take another look at those elimination diets.

  • ALL healing diets start by removing highly processed, packaged “foods” found in the Standard Western Diet.
  • ALL healing diets understand the link between gluten and autoimmune conditions and remove it as well as other grains that act like gluten in the body.
  • ALL healing diets will address and remove additional foods that are known to be inflammatory like soy and for some dairy or peanuts.
  • All the good healing diets will address the needs of the individual and food sensitivities.

So what’s so special special about Paleo and the AIP diet? Not much and they are difficult to maintain. AIP takes a step in the right direction by including fermented probiotic foods but it doesn’t fully address the underlying issue. None of these diets work to fully restore balance to the microbiome. Its not just about what you leave off of your plate-its about what you fill it with and the proportions. My patients enjoy a more flexible way of eating as long as they support the health of their beneficial gut bacteria. Some find they do great on many of the foods other diets may exclude. Others do have sensitivities so we omit those triggers. Its all about you and your specific needs.

Fill your plate with fresh whole foods including fruits and vegetables, fiber rich legumes and whole grains. Microbiome pre-biotic superstars include asparagus, onion, jicama, Jerusalem artichoke, leeks, garlic, radish, carrots and tomato. All are packed with the perfect types of fiber needed to feed our friendly bacteria. Fermented foods like raw sauerkraut, kimchi, fermented vegetables and kefir all contain millions of probiotic bacteria that can help to replenish the good bacteria of the microbiome. Include them at every meal! Taking a high quality broad range probiotic supplement can also do wonders. Pasture raised organic meats, poultry and wild fish are important part of a healthy diet but balance is key. They are a great side dish but be sure to fill up with the superfoods that will nurture your little friends. Take care of your microbiome and it will take care of you.

  1. de Goffau MC1, Fuentes S, van den Bogert B et al. Aberrant gut microbiota composition at the onset of type 1 diabetes in young children Diabetologia.,.2014;57(8):1569-77.
  2. Giongo A, Gano KA, Crabb DB, et al, Toward defining the autoimmune microbiome for type 1 diabetes. ISME J 2011;5:82-91.
  3. McLean M, Dieguez Jr Dario, Miller Lindsey M, Yong Howard A. Does the microbiota play a role in the pathogenesis of autoimmune diseases? Gut doi: 10. 1136/gutjnl-2014-308514
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