The Gut Microbiome's Role in Autoimmune Disease | Chris Kresser
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Does the Gut Microbiome Play a Role in Autoimmune Disease?

by Chris Kresser

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Sebastian Kaulitzki/Hemera/Thinkstock

New research suggests that supporting our gut microbiome may help prevent (and even treat?) autoimmune disease.

This is a guest post written by staff clinician Amy Nett, MD.

Meet Your Microbiome

If you commonly read this blog, or listen to Chris’s podcast, you have undoubtedly developed an appreciation for the trillions of microbial organisms that normally inhabit a healthy small and large intestine. Most of these microbes are bacteria that have co-evolved with humans, depending on us for their survival just as we depend on them for our health and well-being. For example, we provide nutrients for bacteria which then keep our immune system in check, digest certain carbohydrates that would be indigestible to us, and make vitamins and other important compounds that we would otherwise be unable to produce. This wonderful, symbiotic relationship is what makes up your microbiome. A (hopefully) harmonious collection of microorganisms in our guts that aid in so many of our body’s vital functions.

The Microbiome Changes with Disease

Our microbiome can affect us in multiple, profound ways ranging from how we store fat (1, 2, 3) to whether we feel happy, anxious or depressed (4, 5, 6). When the normal gut microbial communities are disturbed, whether you’ve used antibiotics or are suffering from a bacterial infection, it can lead to dysbiosis or small intestinal bacterial overgrowth.

Antibiotics, C-sections, poor diet, and autoimmune disease; what’s the connection?

Dysbiosis is associated with a growing number of diseases such as Crohn’s disease (7), ulcerative colitis (8, 9), irritable bowel syndrome (10), and both type 1 and type 2 diabetes (11, 12). You’ll find that the variety and balance of gut bacteria is often different in patients with chronic inflammatory conditions as compared with healthy individuals. Research now suggests that these diseases are not due to any single bacterium, but from changes to the entire microbiome. And since a large part of our immune system is found within the gut, several diseases resulting from dysbiosis are autoimmune diseases.

What Is Autoimmune Disease?

Autoimmune disease can be thought of as a case of mistaken identity: the immune system targets normal proteins as if they were harmful foreign invaders and becomes overactive. Normally, the immune system responds to a specific pathogen, like a cold virus, and once that pathogen is cleared, the immune system can settle down to its normal state. In the case of autoimmune disease, the immune system often stays on high alert, resulting in chronic inflammation.

With more than 80 different types of autoimmune disease, this class of disease has been particularly difficult to understand: what exactly causes the immune system to attack otherwise normal healthy human cells?

The Three Legged Stool of Autoimmune Disease.

Dr. Alessio Fasano, a world-renowned gastroenterologist, expert in autoimmune disease, and pioneer in understanding celiac disease, describes autoimmunity as a three-legged stool, meaning that three essential components must be present in order for someone to develop an autoimmune disease:

  1. Genetic predisposition: certain genes make individuals more likely to develop certain diseases.
  2. A trigger: specific antigen, or protein, that the immune system recognizes as a threat (real or not), that sets off the cascade of over-activation. In the case of celiac disease, the trigger is gluten. However, in the vast majority of autoimmune diseases the trigger remains unknown.
  3. Intestinal permeability (also referred to as “leaky gut”): this increased permeability means that the normally tightly knit cells of the intestines are weakened and “leaky”. This allows large compounds, such as proteins from food or bacteria, entry into our bloodstream. Leaky gut can occur due to any number of reasons such a food sensitivities, gut infections, or chronic stress.

Does the Microbiome Play a Role in Autoimmune Disease?

Increasing attention is being paid to the importance of the microbiome in health and disease—even slight imbalances have far reaching consequences. It has become clear that the microbiome profoundly affects our immune system, and new research provides insights into how changes in the microbiome can act as the trigger in developing autoimmune disease.

A recent paper reviewed some of the most recent research that the health of our microbiome may be the key factor in whether or not we develop an autoimmune disease (13). Below are a few of the key points:

Two of the most significant autoimmune diseases in terms of global morbidity and mortality are Type 1 diabetes mellitus, and rheumatoid arthritis (RA).

Type 1 Diabetes Mellitus

Type 1 diabetes (T1D) is an autoimmune disease with antibodies that destroy the insulin-producing cells of the pancreas, leading to insulin deficiency and blood sugar irregularities. Most often patients are diagnosed in childhood or adolescence, and there is a known genetic association. However, in studies with twins (who share the same genes), only about 50% of twins both go on to develop the disease. This further supports the idea that the development of disease depends on more than genes alone. For instance, immigrants have a risk of developing T1D that is dependent on their place of residence, not their country of origin.

Studies looking at differences in the gut microbiome between people with T1D and healthy individuals have found the following differences:

  • Children with T1D have a smaller amount of beneficial bacteria.
  • Children with T1D have less stability and diversity of bacteria in their gut.
  • There are significant differences in both bacterial composition and metabolic capabilities between those with T1D and without.
  • After treatments to normalize blood sugar in T1D patients, there was also a return to microbial diversity in those individuals.

Overall, the research is convincing that T1D is associated with a disruption in the normal microbiome. At this time, no single organism is responsible for the onset of this disease. However, in genetically predisposed individuals a disruption of the normal microbial communities provides an environment in which the disease may develop.

Rheumatoid Arthritis

Rheumatoid arthritis affects about 1.5 million people in the United States, and up to 1% of adults worldwide. It is an autoimmune disease that affects many of the joints throughout the body, most commonly the joints of the wrists and hands.

As with T1D, there is a known genetic association.  However, studies with twins again prove that genes play even less of a role in the development of RA when compared with T1D. Research again supports a relationship between the microbiome and the development and progression of RA. Of particular interest is the role of the bacteria living in ones mouth.

Periodontal Disease and RA

  • Patients with newly diagnosed RA have higher rates of severe periodontitis and more tooth loss despite normal oral hygiene compared to healthy individuals.
  • The severity of a patients periodontal disease can be correlated with the severity of their RA disease activity.
  • Specific bacteria that live in the mouth have been shown in animal models to increase the severity of joint disease.
  • Specific bacteria are present in both dental plaque of patients with RA, and in joint fluid.

Many other autoimmune diseases are being studied to look for related dysbiosis, providing increasing evidence that disruption of the microbiome is associated with the development of some autoimmune diseases. Though there is clear correlation between changes in the microbiome and autoimmune disease, causation is not yet clear. This means we cannot say if it is the dysbiosis that leads to autoimmune disease, or if dysbiosis is the result of an overactive and misdirected immune system.

One More Reason to Take Care of Your Gut?

As if we didn’t already have enough reasons to take care of our gut and help our beneficial bacteria thrive, it may be that decreasing our risk of developing an autoimmune disease is one more important reason to be good to your microbiome.

Now I’d like to hear from you: Have you made changes in your diet or gut health that have affected your autoimmune disease? Do you notice flares or exacerbations of your autoimmune disease when you eat certain foods?

Amy NettAbout Amy:  Amy Nett, MD, graduated from Georgetown University School of Medicine in 2007.  She subsequently completed a year of internal medicine training at Santa Barbara Cottage Hospital, followed by five years of specialty training in radiology at Stanford University Hospital, with additional subspecialty training in pediatric radiology.

Along the course of her medical training and working through her own personal health issues, she found her passion for functional medicine, and began training with Chris in June of 2014.  She has recently joined his clinical practice to work with patients through a functional medicine approach, working to identify and treat the root causes of illness.  Similar to Chris, she uses nutritional therapy, herbal medicine, supplements, stress management, detoxification and lifestyle changes to restore proper function and improve health.


Join the conversation

  1. Hi I was never officially diagnosed with narcolepsy but there is no doubt I have it because of my horrible sleep at night and my sever cataplexy. Why haven’t I gone to the doctors about this? I don’t want to jeopardize my career choice by getting diagnosed with narcolepsy. I also have always had the mindset that I can fix my own issues. Recently I have really been researching he connection between narcolepsy and the gut. I have read everything, lectin intolerance, gluten intolerance, histamine intolerance, amino acids, etc; but I have recently moved into probiotics and prebiotics. I have got to say that leaky gut is 100 percent the cause of my narcolepsy and my cataplexy. I notice when I avoid lectins, and gluten I do not have cataplexy which leads me to believe that I have a damaged gut that has caused inflammation and a toxic overload. I am abstaining from gluten and lectins, eat all organic, grass fed, grow my own veggies, and am a complete nut job about it now. It wasn’t until I started consuming Kombucha that I realized that probiotics/fermented Foods/beverages/prebiotics made the biggest impact on my cataplexy. It’s going away! I slip up sometimes however my rebound is decreased less and less every time I do. Meaning the old foods that used to bother me don’t anymore. I assume I had some serious leaky gut and a lack of beneficial bacteria in my stomach which will take a very long time to heal. I just have to keep consuming probiotics in all forms and al different kinds. Also TIGER NUTS!!! They make me feel incredible. The more I research and the more I try what I research the more I am convinced that it’s my gut. Also it’s very obvious that non organic pesticide/Herbacide sprayed foods have the worst impact on me. Glyphosate is proven to kill beneficial bacteria in your gut. Watch out.

  2. I have several Autoimmune diseases. Idiopathic epilepsy which I believe is autoimmune in nature, Hashimoto’s, and A rare disease called relapsing polychondritis. After years of suffering and taking all kinds of prescriptions. And continuing to get worse. I changed my diet. I’ve gone thru a lot of trial and error and I don’t always stick to it. Probably about 90% of the time I do though. I’m gluten free and mostly grain free. Organic and grass fed only. No processed sugar but lots of organic fruit and raw honey. But #1 would be adding milk kefir and fermented vegetables. This addition stopped my relapsing Polychondritis flares. My miracle!

    • Where do you buy the milk kefir and fermented vegetables? I have Relapsing Polychondritis also and have changed my diet as well.

      • Buy milk kefir grains and make your. Lifetime supply that way! And way more probiotics than store bought. I bought mine on just searching for Milk Kefir grains.

    • Hi There,

      My wife (25 yr) is suffering with SLE. Could you please suggest us few tips.. how she can completely cure from SLE.


  3. I was diagnosed with hashimotos thyroiditis app 30 yrs ago. Have been on synthroid or levothyroxine ever since. Recently began to have severe arthritis in my hands and wrists. I also began to have many stomach problems. Began to research autoimmune diseases, and found out that inflammation was causing all of these diseases. I also found out that diet is a huge factor. Am changing my diet, and am hoping this will help.

    • victoria, i have hashimotos and have been on a high dose of Maya Superfood powder for 3 years and now i have reduced my antibodies by 2/3. not sure if its the Maya powder, but because its high in prebiotic fiber, i can say it may have something to do with it. try it! i take 4 tsp/day spread throughout the day…mix it in milk or water and take it like a shot of tequila!

  4. I appreciate the connection between autoimmune health, the gut and diabetes. I see this in my clients with type 2 diabetes who have gluten-allergies or sensitivities and high levels of inflammation.

  5. I was diagnosed with GA (Granuloma Annulare) by my Dermatologist about 4 years ago…a rash that can develop all over your body at any given time. No known cause or cure, at least that’s what I am told. It does not itch or hurt. If you didn’t see it you wouldn’t know it’s there. I am told that it is an autoimmune disease. Steroid cream applied topically will take it away, but hesitate to use this cream as it thins the skin over time. This past winter, the GA seemed to disappear. I was very happy, however, this spring my skin started to develop small raised bumps on my arms and legs and now it has spread everywhere on my body. The bumps eventually turn pink and start to connect and are now turning into the pinky, purple color like before only covering a much greater area. I am very upset about the return of this. Went back to the dermatologist and she has recommended Phototherapy which I am now doing.
    Amy, Could you please give me some advice? I have tried a gluten free diet in the past with no success.
    Please, if anyone may have had this or heard of it make any suggestions for me?

    • I am so desperate to find the true cause of my Granuloma Annularae. I don’t bother with dermatologists anymore because I want to treat the cause, not the symptom. I’ve had GA since I was a child. I have many other health issues and I believe they are all connected, but I can’t find the right doctor to help figure it out. I have hypothyroidism, lower than normal platelet count, occasional enlarged spleen, weak/painful hip joints, halitosis, random nausea, dizziness and stomach pain. I’ve gone to different specialists for all of these conditions separately but they can never find a cause, they just treat the symptoms. I’ve read studies where a concentration of 3 strong antibiotics (ROM therapy) has helped some people with GA, which has led me to think it’s stomach bacteria I’ve been carrying around for years.

  6. Thanks for the post, a very important topic and helpful to many!

    It is absolutely vital to maintain a balanced microbiome not only in people with autoimmune disease, but everyone.

    Although the research is not clear on whether leaky gut contributes to autoimmune (AI) disease, or autoimmune disease contributes to leaky gut, yet one thing is clear maintaining the lining of the digestive tract is imperative to people with AI disease.

  7. Very interesting article, thank you!

    I have Hashimoto’s and cut out processed foods, added sugar and gluten after diagnosis about 18 or so months ago. That definitely helped to manage my symptoms but wasn’t the answer I’d been looking for.

    About a year ago I reduced my hours in what was a very stressful working environment, and then 5 months ago I started following the autoimmune protocol (and also changed jobs). I can’t remember the last time I had a flare and I believe it’s a combination of diet and lifestyle factors.

    It would be interesting to know how my microbiome has changed since making these lifestyle changes but unfortunately I don’t have a “before” test to be able to compare!

    Thanks 🙂

  8. I believe the article you wrote as well as the downloadable ebook “9 Steps to Perfect Health” are excellent, very inclusive, and expland knowledge about the source of many illnesses, but there is one point I’d like to emphasize. The reason I developed a bad case of Leaky Gut Syndrome, which caused a systemic reaction to many food, fungus, and chemicals in the environment (known as Chemical Sensitivity), was because my chronic yeast infection and gut dysbiosis went untreated long enough that the candida yeast changed forms and developed fibers that permeated the gut lining and wall to allow particles of food, bacteria, and fungus into the bloodstream, creating auto pollution, and I developed Chronic Fatigue Syndrome as well from a very depressed immune system. The candida was really the reason my gut became permeable. However, after discovering the source of my problem, I stayed on a meat and vegetable anti-candida diet for a long time, devoid of sugar and fruit and most carbohydrates, and I slowly improved and returned to health. I also took massive amounts of probiotics, dealing with a lot of die-off symptoms from the yeast absorbed in my body, i recovered from CFS, but I still have to be vigilant in order to avoid all sugars, simple carbs, and chemicals due to the damage that’s still in my gut. I’m working hard to improve the lining of my gut with supplements, but I may never have gut integrity competely back again. Thank you, Chris, for all your helpful information. I wish you’d existted when I first became ill! Awesome work!

  9. Hello, I have celiac disease and my sister also has celiac disease and type 1 diabetes. My other sister has no autoimmune diseases she was the only one breastfed. I also have just been diagnosed with blastocytosis Hominis. I defiantly think the gut microbe plays a huge role in autoimmune diseases. We have NO family history of diabetes.

  10. We need to embrace the truth that for anyone that is living with municipally treated water supply that does NOT (in their own home) remove the Chlorine prior to using this water to bath, drink or cook with, is killing off their own Immune System. That Chlorine bleach used to treat those municipally treated water supplies kills off our Friendly Bacteria. That Friendly Bacteria is what maintains our intestinal tract, our GUT. A major portion of the human immune system is in the GUT and all that chlorine is killing off that friendly bacteria, shower after shower. This will also hinder the rebuilding of your immune system by continuing to live with the Chlorinated water supply. Remove the Chlorine with an appropriate filter in your home and greatly increase your chances of rebuilding that immune system and re acquainting your self with health.

  11. hi amy.

    i recently contracted autoimmune hepatitis. i am following the autoimmune protocol with great success. but i worry about my kids because of the genetic component. my doctor recommended an IGG food sensitivity test for my daughter only because she had a couple warts and trouble sleeping. she also has bags under her eyes. otherwise very, very healthy. the panel came back showing sensitivity to all the foods she normally eats. i know this signifies leaky gut. my question to you is can we repair leaky gut without forsaking all these foods? what if we go gluten, diary, egg, soy free and work on taking gut healing supplements and probiotics? all of my reading about withholding foods you are sensitive to involves people who are outwardly so much sicker than she is. indeed she is not sick! and if we heal leaky gut as described above, won’t supposed food sensitivities go away?

  12. I came down with Polymyalgia Rheumatica four years ago at the age of 62. It is an autoimmune condition where the arteries of the arms and legs become inflamed. It is very painful and totally debilitating. The doctor prescribed prednisone for it, and said I would have to take the prednisone for about 2 years. Then they would try to wean me off it.

    Rather than take the prednisone, I eliminated everything inflammatory from my diet, including all meat, dairy, fish, eggs, processed foods, oils, sugar, gluten. That left some whole grains, legumes, veggies, fruit, seeds and nuts, and seaweed. It didn’t work instantly, but by the end of 3 months, I knew I was better. By the end of 6 months, I was well but had to recover all the strength I had lost by being so weak when I was sick. I have continued to eat this whole food, plant based diet since then and am totally well and stronger than I was before I got sick!

    Besides being inflammatory, meat doesn’t feed the microbiome because meat is completely lacking in fiber which the bacteria of the gut depend on. Both soluble and insoluble fiber are found only in plant foods. Meat also slows the digestive process way down, leading to absorption through the large intestine of waste products that should have been expelled. Milk products have the same effect. Besides, plants are loaded with phytochemicals and anti-oxidants that our body can use. Plants contain everything that the body requires including plenty of protein, calcium and iron. The only exception is enough vitamin B12. Apparently though, we do get some B12 from the bacteria in our gut, which is where the animals get their B12.

    • I thought seeds and nuts were inflammatory too. I can see getting b12 from your gut.IF your gut is healthy and you are able to methylate b vitamins…many people with autoimmune disease can’t.

    • I was diagnosed with PMR last June and could not tolerate the intense pain in shoulders, neck, hips and lower back, so I was put on a high dose of prednisone (40 mg per day.) I adopted a vegan diet that excluded, in addition to all animal products, refined foods, processed foods and heated oils. I eat mostly fresh vegetables that alkalize the body (most fruit and vegetables do, especially greens,) nuts and seeds, which I tolerate very well, and I take supplements that are known to be anti-inflammatory. Unlike Barbara, I don’t eat most grains (exception made for quinoa) and I limit my intake of beans and legumes (exception made for lentils and occasionally chick peas,) as these foods tend to be acid forming. I have added superfoods including spirulina, chlorella, and phytoplankton, which I take daily. In addition, I drink concoctions that are recommended for liver detox (including teas made from milk thistle, and drinks made with lemon juice and apple cider vinegar,) adding grated ginger root, cinnamon, and other spices. I take probiotics religiously every day, and I eat fermented foods (e.g. sauerkraut,) with every meal. My main problem is that the prednisone disrupts the digestive process, so I don’t get the full benefit of my diet. Still, 6 months into my diet, I am down to 5 mg a day with much less pain. Barbara’s success makes me hopeful and I intend to continue on this path. Perhaps someone can point out a way to improve on what I am currently doing to speed up my recovery so I can get off the prednisone (if I tried to get off now, the symptoms would come back in full strength.) Worth noting: I have seen great improvements in my good cholesterol, blood sugar levels, triglycerides, blood pressure, and weight loss.

      • Danielle, your approach sounds really good to me. I actually eat mostly quinoa and millet for starch which are really seeds and not grains. I ate many of the same herbs as you, especially lots of ginger and turmeric. And I upped my intake of Vitamin D to 6 drops of liquid D per day in winter. I think it helps. My doctor wasn’t interested in my experiment, but he gave me a prescription for a monthly C reactive protein test so that I could track my inflammation level. I often took 2 ibuprofen tablets a day to handle the stiffness and pain until it was gone (about 6 months).

        My goal was always to calm my immune system. Because of your great blood test results, you may find that you can wean off the prednisone more easily than many other people have been able to without a rebound. I also found that my weight dropped on this diet and my total and LDL cholesterol levels dropped to normal for the first time since I started having it tested over 10 years ago. Nice side effect!

      • Danielle,
        May I suggest you add some homemade bone broth to your regimen? It will heal your gut and give you much needed protein and healthy fats. If you do decide to do this, please make sure the animals you use to make your broth were pasture raised with no hormones or grains in their diet.

      • i wish 40mg were a high dose. i’ve been on 160iv. it has slaughtered me and after being on high-dose prednisone for over a decade, i can’t seem to get below 5mg. i am a vegetarian (supplement w/coconut yogurt + probiotic supplements), have long cut out gluten, dairy, &sugar (i get about 18g TOTAL a day mostly from veggies). would love advice. also not all nuts/seeds are inflammatory.

      • Thanks for your concern Wendy. I used to have the same kind of ideas about a vegan diet – not enough protein, not enough calcium, etc. etc. But I have taken several nutrition courses, tracked and analyzed my food for a week twice and found that I get enough of everything including zinc, with the one exception of Vitamin B-12. I eat whole foods, not junk food or processed foods. That makes a big difference. A whole food, plant based diet is completely adequate. Pumpkin seeds, sesame seeds, cashews, lentils, oats, nutritional yeast – these are all good sources of zinc.

        I have been told several times in the nutritional courses that I have taken that one should be very careful about zinc, copper, or iron supplements (i.e. do not take them or supplements containing them without a doctor’s advice) because these metals have been implicated in the development of Alzheimer’s Disease.

        From the NIH (National Institutes of Health) website, here is a link to an article called “The Role of Zinc in Alzheimer’s Disease”:

        “Zinc, in addition to copper and iron, has been shown to be involved in AD. Here, we review the current literature relating to neuronal zinc metabolism and the way in which zinc can modulate normal brain activity. We discuss also the contribution of zinc to the formation, aggregation, and degradation of the amyloid-β (Aβ) peptide and the contribution of zinc to the pathogenesis of AD.”

  13. I am 78, was diagnosed w/ RA 3 years ago but had few symptoms and didn’t understand the import of the test result so ignored it. For the past several years I have been getting weaker and have lost much of my usual energy, have had balance problems and most recently developed pain in wrists, hands, ankles and feet. My hands were so weak I couldn’t open jars, use a can opener. Another test showed RA and this time I looked into it. I realized the standard treatment for RA was just plain bad and did not address the cause of the RA. So I started doing research. I learned about leaky gut and started on daily bone broth, about a cup/day. That was 3-4 months ago and my energy levels are back to the high level I had been used to, I have only a slight twinge now and then in my wrists, all else is fine, a problem with my left knee is at least 60-70% better, balance problem gone. Prior to the bone broth I had constant urges for sweets and had gained weight. I’m eating less now, am not always hungry as I had been and my urges for sweets are minimal. I’m losing weight. I think that I was losing nutrients because of leaky gut and that’s why I was hungry all the time and lost energy and strength and ate sweets for a quick energy boost. I’m able to hike the redwood trails again and loving it.

    • Hi Sylvia,
      I hope you get this, after reading I have same problems in my wrists that you had. I am 35 and strugging with everything and more recently my right foot has swelled. I got a rough diagnosis last week ‘inflammatory arthritis ‘ is best my doctor could do. I have tested negative for RA but symptoms stil point to it, the doctors are a nightmare with these things.
      I am wondering really what sort of pain you had in your wrists are I too cannot open jars, cans and have difficulty even buttoning my jeans together. Im looking into this diet as I really don’t want to take the strong meds they have given me , methotraxate . Have your wrists got much better now ? many thanks Vicky

  14. Reminds me of one of the House Md. episodes where they cured a porn star, it turned out to be autoimmune, but funny thing is that it was when they removed the worms that the patient got worse, turns out that these worms kinda help with taming the patient’s rare iutoimmune disease.

  15. I could write on book on my struggles, but I doubt anyone would read it (LOL!). So I’ll summarize first by saying that I am a total believer that gut health is hugely important.

    5+ yr ago: SAD, mild depression, arthritis, gum disease, adult acne and rosacea. In denial that there was anything wrong with my high-carb diet.

    2yr ago: tossed wheat and dairy under the bus. Arthritis cleared up and have fully regained pain-free use of my right arm.

    6mo ago: Eczema flared; scalp looked like ground beef. At the same time, chronic bloating and flatulence reached life-altering level.

    Today: I eat as though I were a Type II diabetic, and supplement with Vitamin D, fish oil and the best probiotic that I have found so far. I also regularly use ketoconazole shampoo. Everything is much better, even my gums don’t bleed anymore. No SAD this winter, either. Crossing my fingers that I can avoid regressing.

  16. There is a new documentary called ‘Microbirth’ whose cast of characters reads like a Who’s Who list of major microbiome researchers. ‘Microbirth’ explains that mode of delivery and feeding (breast or formula) hugely establishes our microbiome and subsequent disease status is provided. Those implementing healing diets and achieving remission of chronic disease likely are changing that very resilient stable microbirth microbiome (which has been altered due to lifetime exposures such as antibiotics, heavy metals…) Dr. Rob Knight of the American Gut project repeats: long term diet likely can change up a very stable resilient microbiome, which is likely why SCD/GAPS/PALEO/AIP works for so many. The links to the ‘Microbirth’ documentary are: . Dr. Rob Knight’s latest findings of the American Gut data (I have given permission to permit the reprint of this article in the UK CAM magazine) are:

  17. Dear madam/sir,
    I am kumar,male,aged about 54 years.I am residing in chennai,India.I have been battling with giardiasis for about 25 years and gastritis and other related problems such as loss of appetite,chronic malabsorption of food,indigestion,falling of mucus,constipation,upset stomach.Can the probiotic called prescript assist cure all my above cited miseries?Can anyone throw some light on the above.I shall be highly indebted to them,
    With regards,

    • Giardia can be treated with a course of antibiotics, usually this is quite straightforward. I’ve had this myself, what a foul thing it is, I wish you the very best recovery!

  18. I had chronic eczema for 2 years and my son nephrotic syndrome. We started on the GAPS diet almost 2 years ago now. My eczema has all cleared up and my son is fighting fit!

  19. It may be important to mention that we have not yet characterized what a “normal” or “healthy” microbiome for humans actually is. However we do have some clues….

    The most important point (so far) seems to be that:

    – gut profiles are better characterized at the level of the different bacterial communities (i.e. many different bacterial strains grouping together) and how they relate to one another – not by counting up individual strains and correlating those with disease/health.

    – A core of enterotypes (not strains) are starting to emerge although many contradictory findings are still the norm, not the exception.

    – as pointed out in this article, the question “Do gut changes follow disease or is it the other way round? (& for which diseases, specifically)” cannot be answered without having a solid foundation for what is “common”, “normal” or “optimal”.

    • Raphael, I’m not a microbiota expert, but have read much and written some about it. My takeaway is that the science on this is still pretty new; meaning that there’s no definitive conclusions about how all the “strains” in the human GI tract affect health.

      Given that, as you say, there are contradictory conclusions, which is the norm for health matters. Consider that we still debate the health impacts of coffee, fat, meat, vegetarianism etc.

      Your last bullet point speaks to causality vs correlation, another theme threaded in every scientific study related to health and disease. On this point, though, several studies are pretty conclusively indicating that “unhealthy” bacteria strains cause and/or or contribute to certain maladies, such as inflammation, leaky gut and (strangely) depression.


      • The question that is of most interest to my mind is whether the microbiome is more of a ‘reactive’ organ (as DH Kiefer put it) or not. If you consider the analogy of our bodies being the soil for bacteria, then the health of the soil should play a primary role in the health of the bacteria and vice-versa – but maybe to a lesser extent.

        You’re correct, certain individual strains of bacteria are casually related to diseased states. However, putting this into perspective by considering the total number of fungi and bacteria in our guts, this turns out to be a minuscule %. The key point is the mechanism of horizontal gene transfer and other gene trading strategies. Looking at their genomes gives us a clearer picture of how they interact with us than looking at the kinds of individual strains do.

        Vegetarianism is a political and moral ‘thing’ which has no basis in science. Coffee is great (sans the other bad chemistry that may accompany it) and the tiniest of fractions of people may not bode well on coffee specifically. Meat is the stuff of life. Shitty meat is, well, shitty meat. Fat is essential and it is not the same as CHO but bad fat is, well, bad.


  20. I have been diagnosed with Psoriatic Arthritis. I changed my diet to raw with no sugar, honey, agave for 7 weeks. The elimination of all animal products helped my joints as did losing 10 lbs. I finally gave up coffee/caffeine and got more relief. I still have pain. I now eat a vegan diet with whole grains like farro and quinoa for another month. I discovered that brown rice gave me congestion?

    My question is: Should I cut out gluten? I am feeling better on the vegan diet, but I want the PA to go into remission without methotrexate.

    • Hi Debbie,

      It is wonderful to hear that you’ve already made so much improvement in your symptoms with dietary changes. As you likely know from reading other articles on this site, we do find the most success (both in clinical experience and with our own personal experience) following a Paleo template dietary approach. Thus, I would suggest you remove gluten, at least for 30 days, and see if you notice further improvement.

      Though discussed in great detail in other articles, in Chris’s book, and on a myriad of other web sites, in brief, we recommend avoiding gluten-containing grains given that 1) grains have poor nutrient content, and do not contain any nutrients that cannot be obtained elsewhere in the diet, and 2) many grains contain proteins capable of provoking an immune response or allergic reaction. In particular, several studies suggest that gluten may have negative effects on the intestinal barrier contributing to leaky gut, and allowing larger, unwanted compounds access to the bloodstream. Again, if we think of doors between the intestinal cells, gluten can open those doors even in people without celiac disease — in most people those “doors” may be open for such a short time that most often the result is inconsequential. However, we also know that some people become intolerant to gluten later in life, and it is not yet clear what causes this shift from tolerance to intolerance.

      If you do want to include some gluten-containing grains as part of your diet, you might want to consider testing for gluten sensitivity with something like the Cyrex Labs Array 3 panel, which is one of the most comprehensive tests for assessing wheat and gluten sensitivity. If you do not show any antibody production on such a test, then you may consider keeping grains as part of your 80/20 rule. But again, grains have such low nutrient-density, that even despite the potential toxicity of gluten, there seems little reason to make them a regular part of your diet.

      • And…what about the OTHER parts of the paleo ideas? The nutrients in animal foods that this person is missing? Simply cutting out gluten from this person’s already severely limited diet doesn’t add in the nutrients she/he is missing. Bone broth, properly raised meats, fermented dairy etc.

        • Steve,

          I agree that there are many other benefits to a Paleo-type diet, aside from removing gluten. And particularly, as you mention, bone broths and meats from grass-fed, pastured/free-range animals provide incredibly nutrient dense sources of a number of vitamins and minerals. And in general I do encourage eating such animal products. However, it’s also important to me to recognize each person’s individual preferences, and given that Debbie has made a conscious decision to follow a vegan diet (and seems to feel some benefit on that diet), I prefer to respect her choice in that matter. Since she specifically asked about gluten, I directed my reply accordingly. But you are correct in that most people benefit significantly from eating a more varied omnivorous diet.

  21. I have RA and I’m keeping it in check with paleo/AIP diet; no meds. Lots of bone broth for healing the gut. Since reading this article, I believe my oral hygiene must be contributing. So, how do I find out what is the specific bacteria damaging my joints and what is the antidote? Thank you for this article.

    • Dr. Scher’s latest R&D which updates the RA microbiome findings was published in, “Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis,” Scher et al., Nov 2013. His works, and related podcast, is referenced in the article which you may want to read.

      Dr. Scher is the Director of the Microbiome Center for Rheumatology and Autoimmunity-MICRA at NYU Langone Medical Center’s Hospital for Joint Diseases, and Director Arthritis Clinic NYU Hospital for Joint Disease, New York University School of Medicine. He now recognizes and promotes the paradigm shift connecting the gut microbiome bacterial community and arthritis.

    • Hi Maureen,

      I’m glad to hear that you’re able to manage your symptoms with diet. I’ve found the research on arthritis and oral hygiene (specifically that related to Porphyromonas gingivalis) particularly interesting and compelling. There is certainly hope that we may soon be able to identify the specific pathogenic bacteria and employ a targeted treatment. However, at this time I don’t yet know that this emerging science gives us a clear and distinct path for treatment.

  22. Diagnosed with UC early 2012. All meds failed. Started researching the Human Microbiome Project and work by Rob Knight at Knight Lab in Colorado. Implemented specific carbohydrate diet in November 2013 and have been symptom free and med free for 1 year. Will continue to follow diet for more years to fully reset gut microbiota and immune system. Currently studying nutrigenomics and biochemistry.

  23. When I eat gluten and dairy for a few days in a row, besides getting total body swelling of about 15 lbs of fluid, I also start to slur like I’m drunk. As well, I learned in one of the Summits that for people who have Hashi’s, their TPO anitibodies will attack their cerebellums and that is the reason you get forgetfulness, fogginess and muscle loss (all of which I have). The slurring is also related to that, and is pretty scary, considering it’s such a neural type thing…. You can check for cerebral damage two ways: an indicator of minimal damage is to stand with your eyes closed and then try to walk toe to heel. (must have your eyes closed to bring the cerebellum in to play). If you get extremely unbalanced and nearly fall…you have some minimal damage to the cerebellum. Then, an indicator of more moderate damage is “termination tremors”. If your hand shakes right at the end point of reaching for something, then that’s the sign of moderate damage. The best way to test, is to put some peas on a fork, then try to put them in your mouth. If you shake right at your mouth and the peas fall off the fork….that’s your sign. (that’s how I first noticed it on me). I failed both signs. Learned these tests on one of the Summits. The good news is, you can help your cerebellum by doing crosswords and special things like that. Not sure if you can fix the termination tremors…they didn’t say. Obviously, you need to fix your gut, etc to stop the continued damage…..

  24. Amy,

    I’m impressed with this great summary of the research findings. It’s fascinating how many of the research findings you site for RA and T1 & T2 diabetes are similar to Crohn’s and ulcerative colitis. A twin is 50% likely to get IBD if the other has it. Immigrants are more likely to get IBD if they relocate to a western city. And the composition of microbes are implicated as a major factor in the status of IBD.

    I’m editing my documentary about empowered patients with Crohn’s or ulcerative colitis who use controversial alternative treatments when nothing else works. The patients who do well enough to even stop all their conventional medications all have done a variety of things to rebuild their gut microbiome. Usually through SCD or GAPS. I myself found great benefit from both. I absolutely must keep stress low and stay away from refined sugar.

    Glad to see you mention Dr. Alessio Fasano’s work, it’s excellent.

    • Hi Reid, When do you estimate completion for your documentary? There is a new documentary called ‘Microbirth’ whose cast of characters reads like a Who’s Who list of major microbiome researchers. It would be interesting to understand your film’s participant microbirth history (mode of delivery and feeding) and if there is correlation to success of gut healing. As Dr. Rob Knight repeats: long term diet likely can change up a very stable resilient microbiome, which is likely why SCD/GAPS/PALEO/AIP works for so many. The links to the ‘Microbirth’ documentary are: . Dr. Rob Knight’s latest findings of the American Gut data (I have given permission to permit the reprint of this article in the UK CAM magazine) are:

    • Reid,

      Thank you for the additional input — there is so much fascinating research with autoimmune disease that I hope to write a few more articles about the topic. It is starting to seem that there may be more similarities between these more than 80 different forms of autoimmune disease than was previously appreciated.

      And, I’m glad you mentioned that keeping your stress levels in check is an important piece in your health! I couldn’t agree more, and think tending to stress may be of equal importance to diet when it comes to successfully managing autoimmune disease.

      I’m looking forward to seeing your documentary! Do you have a title yet?

  25. I have suffered from worsening arthritis for ten years or more, and use a cane to get around. and was recently diagnosed as having type 2 diabetes. That was the final kick in the butt for me to take back my health.
    Three months ago I found a functional medicine-based ND who started me on digestive enzymes + vitamins for diabetics, natural anti-inflammatory supplements, probiotics, prebiotics, and I removed sugar, grains and most dairy from my diet. I’ve lost 35 lbs, I am not swollen anymore, my joints move better, my gastro-intestinal system no longer upset. Not only do I feel better, I feel connected to my body and master of my health for the first time – maybe ever!

  26. As always- incredible information. I have been discussing the micro biome a lot with clients. Is there an article that easily describes what the microbiome is. We have many throughout the cavities in our body- not just the gut and would love an easy to read bit to give clients.
    On antithetical note. I am very interested in traumatic events and how the overload of stress to the system can ignite an autoimmune response. – thoughts? Thank you!!

  27. I was diagnosed with mild pancolotis Ulcerative Colitis two years ago and unfortunately have progressed to severe pancolitis even after following Paleo for a year. Since my recent diagnosis I have switched to AIP Paleo and am currently tapering from steroids. I believe that I will have to be AIP for about a year or so before I truly evaluate if the diet is helping. Since diagnosis I have been extremely sensitive to sugars of all types; heavily sugared fruits all the way to the so good but bad for you white stuff. But, even after having cut sugars out with Paleo I still have autoimmune flares. So, I don’t think my flare triggers are food related, but more hormonal related.

    • Katherine,

      I hope you find success with the autoimmune Paleo diet. And your experience with sugars, even including fruit, is consistent with the research that suggests some people with inflammatory bowel disease (IBD), including UC, may do best with a therapeutic, very low carbohydrate diet. Though very low carbohydrate diets can have a negative impact on hormonal balance and adrenal fatigue syndrome, it can sometimes provide substantial benefit in healing the gut for people with IBD.

      If you continue to have UC flares even on a very low carbohydrate diet, you might want to monitor if these are associated with increased stress (such as a few nights of inadequate sleep, or job stress). Stress can also profoundly affect the immune system and perhaps this plays a role in some of your flares?

  28. I had Graves’ disease, an autoimmune disease for 2 years, and after following a natural treatment protocol focusing on the gut, my graves went within 5 months. Since improving my gut health I feel better than ever.

  29. I’ve often wondered if someone with autoimmune disease, diagnosed or not, would be LESS likely to get common colds and flu-like illnesses, because their immune system would be, as you say, in overdrive? I rarely get sick; in fact, the only time I get sick is if I’m sitting in a cold space for too long – then I will almost always get a cold. But, it will be gone in a day or so. So, am I healthy or unhealthy? Eating lots of fermented vegetables and juices here, by the way. But this pattern has been true for me starting long before my diet change.

    • I was told by my doctor that rice is bad for people who are pre-diabetic. Then, recently, I found this diet or food chart that said rice is healing for the pancreas. I usually eat long-grain white Uncle Ben’s Rice. Brown rice is full of arsenic. What is your take on this?

      • They said “rice is bad” because it’s a high glycemic food (it’s pretty much like candy….). Whether it’s good for the pancreas or not isn’t important if you are pre diabetic or already diabetic…it is high glycemic and you shouldn’t eat it. Not only that, most of us shouldn’t eat it. It’s a carb and basically sugar…. makes all of us fat. Not to mention it’s full of arsenic. There’s no real good reason to eat it.

      • They said “rice is bad” because it’s a high glycemic food (it’s pretty much like candy….). Whether it’s good for the pancreas or not isn’t important if you are pre diabetic or already diabetic…it is high glycemic and you shouldn’t eat it. Not only that, most of us shouldn’t eat it. It’s a carb and basically sugar…. makes all of us fat. Not to mention it’s full of arsenic. There’s no real good reason to eat it,. except that it’s sweet and tastes good….

        • An opposing view is found in the book by Paul Jaminet, PhD: “The Perfect Health Diet”. Rice isn’t just like candy.

      • Just my take on this. The Japanese eat rice and live longer than we do. Of course, there are other great things about their diet. If rice is like candy and full of arsenic it doesn’t appear to be affecting them.

          • Actually, the Japanese don’t eat a ton of veggies. Vegetables and fruit are incredibly expensive in Japan (they have to import the lion’s share). They eat rice, fish, and seaweed. My daughter lived in Japan for a year and a half, and observed that in fact the women there hardly eat at all (trying to stay thin when their primary food, rice, is fattening). In fact, they are so undernourished that they can’t make it up a flight of stairs, and have to take the elevator. The Japanese, in general, also don’t exercise, by and large. So, be careful assuming that we should emulate the Japanese lifestyle.

    • You won’t “not get” colds, just because your immune system is in overdrive. What would happen is that you wouldn’t be able to fight it off….and it could develop into worse things.

      • This is true–my arthritis (juvenile when diagnosed) didn’t prevent me from getting all the typical childhood maladies that our vaccines protect us from today. Even after passing through those, I still got sick every single winter (everything but flu).

        What prevented me from getting sick was cleaning up my diet–a wonderful by-product was getting a healthier mouth out of the deal.

      • I see – that makes sense. Thanks for that. I’ve been on a paleo type diet for a long time, including fermented vegetables. I lost a lot of weight years ago, and while I’ve kept it off, ate horribly, tons of sugar, little nutrient dense foods, almost zero protein, and plenty of antibiotics for dental work. The result was extremely low energy nothing seemed to help, including finally eating well, including supplements.

        BUT – since I added fermented vegetable JUICE, there has been a marked difference in my energy levels. I haven’t felt this great in years, and this juice is the only change I’ve made. Interesting! I’m hoping it’s not a fluke and it last.

    • I have noticed the same thing about myself. Rarely sick. But I hurt everyday and have what feels like a sunburn (sometimes it gets worse and sometimes it’s mild, but it is always there.) I have endometriosis and my doc thinks I have fibromyalgia.

      • Liz, could you possibly have a very mild case of Complex Regional Pain Syndrome? Probably not but you might look into it. I had a “mild” case of it and I felt like I had a mild sunburn as well. It is rare enough that most docs have not run across it in their practice.

          • Liz, physical therapy is the only thing that can get one over a case of CRPS so that is what I did. It is a very weird disorder and can be quite severe and painful for some people. Mine involved one arm plus the sunburn feeling. Both have been resolved because of the physical therapy so yes, the sunburn sensation has gone away.

    • I’m with you. I never get sick and its always been this way. I may get one cold every couple of years but its rare. Its strange cause in so many ways I am not well (Hashimoto’s related), but my immune system seems to be made of iron! I’ve always wondered why this is.

    • Hmmm, that is interesting Debbie. I have a sister who has MS and she rarely gets any other type of illness. But then I rarely get sick either and like you, get over it quickly if I do and I don’t have an autoimmune disease. At least, not that I know of.

    • Debbie, from my understanding pl with autoimmune disease would be more likely to get sick. When your immune system is in ‘overdrive’ important components of our immune system are depleted. Furthermore, your bodies ability to respond to the invading organism is slowed.
      Atleast this is the case in SLE according to the reading I have done. I know personally I tend to get sicker than others, for longer.

  30. In my case there was clear causation between micro biome and developing an autoimmune disease. My children and I had traveller’s diarrhea and a few weeks later I had ulcerative colitis. Most people I know with UC had a gut infection right before developing UC.

  31. My reading on the matter of developing beneficial gut microbiota lead me to what I call the “4 Ps”: probiotics, prebiotics, phytonutrients, and — strangely — pea protein.

    Each of these “Ps” supports the growth healthy gut bacteria, particularly the lactobacilli and bifidobacteria strains.

    This article lays out the details:

    Of course, you may not have the time or interest to comment, but I wonder if this point of view underscores your own, Dr. Nett?


    • I presume the pea protein acts like a resistant starch here. Most of the time that fourth “P” would be potato starch (unmodified).

    • Joe,

      In general yes, I do share your view that prebiotics, probiotics and diet are each essential in nurturing a healthy gut microbiome. I might add stress management as another potential key to gut health, but that might not flow well with the “4 P’s” concept. Looking at your article I would also suggest that consuming a variety of prebiotics is most beneficial (and if you read my earlier article on resistant starch you might already know my own bias).

      Regarding phytonutrients, I agree that a wide variety of fruits and vegetables are probably the most important ingredient in a healthy diet. I suspect that many of these benefits may even go beyond the isolated nutrients you specifically mention in your article, given the research that shows it’s often only the whole food, rather than isolated nutrients that provide health benefits.

      But specifically regarding isoflavones in soy, I think there’s enough research to warrant caution in recommending soy (at least non-fermented soy products), with studies suggesting that soy isoflavones contribute to subfertility, or infertility in both men and women, contribute to hypothyroidism, and may stimulate growth of cancer cells. Chris previously wrote an article on soy if you’re interested in a reading a brief summary:

      Pea protein is something I’m not as familiar with, but looking at some of the research, there does seem to be potential benefit — I will have to look into this one a bit more and get back to you!

      • Impressive, Dr. Nett, that you’re taking the time to address so many commenters’ comments and questions.

        Agree w/ you regarding soy, and should have mentioned it myself in my article. I’ve already read Chris’ soyploy; in fact, mention him and his work frequently on my site.

        Ciao for now,


  32. re: MMS

    I disagree with Joanna, the person/s who wrote the wiki article about MMS might not have even ever tried it. There is tons of anecdotal evidence around, healing centres around the world who work with MMS healing people from malaria and many other diseases. The reason there is no “proof” is because only big pharma has the money to conduct trials and as MMS is so cheap tp make they have no interest in it. Also MMS is a threat to them as its so powerful. Matt, i would go to the MMS forum if you havent all ready and learn about it there. It isnt a panacea but it is a powerful tool in clearing the body of toxins. No one has ever died from taking it. Just my thoughts.


  33. Hi Amy and Chris,

    I have had SLE and Lupus Nephritis for 16, as well as hypothyroidism (18 years) and Osteoarthritis and Osteoporosis (2 years since diagnosis). I began cutting inflammatory foods out of my diet a year ago, and have been following the autoimmune Paleo diet for the last 6 months (including fermented foods). I have also removed as many toxins out of my life as possible including fluoride (and other nasties) from drinking water and toothpaste, aluminum from deodorant, replacement of alamgam fillings and pesticides, and am supplementing with many vitamins, minerals, fish oil and probiotics. My blood results are looking amazing and I am now off all 10 of my medications including prednisone, thyroxine and 2 blood pressure medications. I have abundant energy and have lost 7kg body weight without trying. So yes, I agree with your hypothesis that healing the gut can heal autoimmune conditions.

    Thanks for your website, it is a wealth of information for those of us taking our wellbeing back into our own hands.

  34. My father has a autoimmune kidney disease and when he was so affected with a long diarrhoea, he started to take L. reuteri and become much better. When he sometimes has a little episode or diarrohea he usually takes this probiotic and suddenly start to feel better.

  35. The “three legged stool” sounds probable as a cause of autoimmune conditions. So the question is: does it also work in reverse? What happens when you take one or two of the legs away? Obviously the genetic leg can’t be removed, but eliminating the protein trigger and/or the leaky gut should be enough to “cure” an autoimmune disease.

    • Sam,

      Essentially yes…if the trigger is removed or the gut is healed, then most often the immune system should be able to return to a more normal state, thus relieving symptoms, or putting the disease into remission. Because, as you noted, the genetic predisposition for the disease is not removed, I would be reluctant to use the term “cure.”

  36. Hello Amy

    I’ve been reading about the Miracle Mineral Solution (MMS) aka chlorine dioxide.

    Jim Humble says that it selectively kills pathogenic organisms only. He’s used it to cure malaria in Africa.

    What are your thoughts on it?

    • Matt, check out the Wikipedia article on MMS, it sounds like it may be toxic, and that there is no proof of the claims that it cures anything. Would be very cautious about using it.

      • Do you think that perhaps the bodies PH has a role in digestive health also? And if so, in your opinion, what should it be for optimum health? (and how would you test it?)

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