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Does the Gut Microbiome Play a Role in Autoimmune Disease?


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

gut health and autoimmune disease
What is the connection between gut health and autoimmune disease?Sebastian Kaulitzki/Hemera/Thinkstock

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.

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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.

Amy Nett

About 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. She works with patients through a Functional Medicine approach, working to identify and treat the root causes of illness.  She uses nutritional therapy, herbal medicine, supplements, stress management, detoxification and lifestyle changes to restore proper function and improve health.

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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 Amazon.com 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.

    • I hate to be the one to inform you, but if you eat a vegan diet, eventually you will become zinc deficient and copper toxic, which will cause weak veins. The body uses zinc to repair arteries and other tissues, which you cannot get enough of on a vegan diet. While you may have improved initially, you may begin to worsen at some point. http://liveto110.com/copper-toxicity-syndrome/

      • 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.

    • Is adding bone broth the only thing you did to improve your health? (trying to improve my own, tho I don’t have RA)

    • 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: http://biomeonboardawareness.com/microbirth-every-parent-needs-to-view/ . 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: http://biomeonboardawareness.com/optimal-microbiome-diet-from-american-gut-data/