The Autoimmune Solution Pillar I: Heal Your Gut

February 13th, 2015

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The Autoimmune Solution Pillar I: Heal Your Gut

This is the first part of a four part series, based on The Autoimmune Solution. Read the other parts here:

Pillar I: Heal your gut.

Pillar II: Get rid of gluten, grains, and legumes.

Pillar III: Tame the toxins.

Pillar IV: Heal your infections and relieve your stress.


When a patient comes to see me for the first time, I play the role of detective. Each little tidbit of information revealed as they tell me their story is a clue to how they wound up where they are now: sitting in my office with unexplained fatigue, mysterious pain, or any other vague, inflammatory symptoms. Some have already racked up a collection of autoimmune diagnoses only to find themselves still searching for options.

No matter what or where the symptoms are, I want to find out what’s causing them. My treatment approach, The Myers Way®, is about preventing and reversing autoimmunity by getting to the root rather than managing the symptoms.

In The Autoimmune Solution, I explain how genetics only accounts for about 25% of your risk for developing an autoimmune disease. The other 75% is your environment. There are five environmental factors in particular that can put you on the autoimmune spectrum or push you over the edge into full blown autoimmune disease: an unhealthy gut, poor diet, toxins, infections, and stress. I address these five factors with  the four “pillars” of The Myers Way®:

Pillar I: Heal your gut.

Pillar II: Get rid of gluten, grains, and legumes.

Pillar III: Tame the toxins.

Pillar IV: Heal your infections and relieve your stress.

I always start with the gut, even though most of my patients aren’t coming to me with digestive complaints. After all, rheumatoid arthritis is a joint problem, not a gut problem. And what do brain fog, fatigue, and anxiety have to do with your gut? But the first pillar of The Myers Way® is “Heal Your Gut” for a reason. What happens in your gut is vitally important for the rest of your body—if your gut isn’t healthy, then neither are you.


Why is Healing Your Gut Pillar 1?

Your gut is the foundation of your whole body’s health because 80% of your immune system is located there. Without a healthy gut, you can’t have a healthy immune system. Without a healthy immune system, you’re open to infections, inflammation, and autoimmune disease.

It’s the place in your body that interacts with the outside world more than any other, taking in nutrients from food and keeping out bacteria, pathogens, and undigested food. When your gut loses the ability to discriminate between the good and the bad, you have a “leaky gut.”


What is a Leaky Gut?

The gut is naturally permeable to very small molecules in order to absorb nutrients in your food. In fact, regulating intestinal permeability is one of the basic functions of the cells that line the intestinal wall. In The Autoimmune Solution, I explain in depth how diet, toxins, medications, infections, and stress can cause these tight junctions to break apart. Once these tight junctions get broken apart, you have a leaky gut.

When your gut is leaky, things like toxins, microbes, undigested food particles, and more can escape from your intestines and travel throughout your body via your bloodstream. Your immune system marks these “foreign invaders” as pathogens and attacks them. The constant onslaught of inflammation from your immune system causes a widespread immune response throughout your body.

Pillar I: Heal Your Gut


Pillar I: Heal Your Gut


A Four-Step Approach to Healing The Gut

In The Autoimmune Solution, I walk you through the details of my four-step approach to healing the gut. I’ve highlighted the steps below, but they are outlined in much greater detail in The Autoimmune Solution.

  1.   Remove the bad. Get rid of things that negatively affect the environment of the GI tract, such as inflammatory and toxic foods, and intestinal infections such as yeast overgrowth and SIBO. There are quizzes in The Autoimmune Solution that will help you determine whether or not you could have one or more of these infections.
  1.   Restore the good. Add back the essential ingredients for proper digestion and absorption, such as digestive enzymes, hydrochloric acid and bile acids. Aren’t sure which ones you need? I cover this subject in more detail in The Autoimmune Solution.
  1. Reinoculate with healthy bacteria. Restoring beneficial bacteria to reestablish a healthy balance of good bacteria is critical.
  1.   Repair the gut. Providing the nutrients necessary to help the gut repair itself is essential. L-glutamine is an amino acid that will help mend your gut lining. Drinking bone broth or collagen will also help to heal your gut, as will supplementing with omega-3s, zinc, and herbs such as slippery elm and aloe vera. For a more extensive list, there is a supplement guide in The Autoimmune Solution.


From Gut Health to Total Health

With The Myers Way®, I look at the many ways that seemingly unrelated factors come together to create a state of health, or a state of disease. Even when your symptoms seem like they have nothing to do with your gut because they manifest in other parts of your body, remember that your gut health affects your total health. That’s why I made it the first pillar in The Autoimmune Solution–healing your gut is the first step toward regaining your health.

I outline my entire 30-day plan to prevent and reverse the full spectrum of inflammatory symptoms and diseases in The Autoimmune Solution. It’s the same approach I use in my clinic and with which I have successfully treated thousands of patients. So what are you waiting for? Start living your solution today.

Next week, I’ll explain how diet can affect your risk for autoimmune disease with The Autoimmune Solution Pillar II: Get rid of gluten, grains, and legumes.


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  • Amanda

    What’s the best lab test to detect Leaky Gut- Cyrex??

    • Dr. Amy Myers

      I use clinical judgement. There used to be a test from Dunwoody labs to test for Zonulin but they are not producing it anymore

    • Hi Amanda, if you have any kind of autoimmune disease it’s safe to assume your gut is leaky already. Either way, these suggestions will help you prevent any problems in the future!

    • Basically, I use clinical judgement. There used to be a test from Dunwoody labs to test for Zonulin but they are not producing it anymore

  • bonnielou

    What’s so bad about legumes? They’re high in protein, fiber and B vitamins. Which legumes have the least lectins? Are they removed by soaking, sprouting or cooking? What should vegetarians eat instead of legumes? What about organic peanut butter?

  • Hi Anita, I run a practicing clinic and do my best to answer questions on here! Did you have a question?

    • Carol Allison

      Dr. Myers, THANK YOU for all the questions you answer by internet and for all of the valuable information you always share along with so many other websites and podcasts 🙂

  • Cathy

    Since we don’t have any functional drs. In the area, will an Endo run the tests for Candida overgrowth, parasites, and low stomach acid etc?

  • Simone

    I know I have a gut infection from lab results ( cryptosporidium) and chronic candida. I am extremely sensitive to supplements and react to almost everything. Is it best to treat infection through the use of antibiotics and then go on to repair the gut?

    • Yes, it’s best to clear the infection first (although I can’t advise a specific medication over the internet.)

      • Simone

        Are you able to advise for someone who reacts strongly to almost everything whether to go the antibiotic route or herbal? not a specific medication. Please and thank you

  • barb

    what does one eat then when they can’t eat anything??? the only way I am not sick is if I eat only chicken/green beans/beef day in and day out to which I become anorexic and sickly looking. What is a person to do then???? I am sooo frustrated with drs. not helping me. what do you charge for a Skype and to look at my 23andme?

    • Hi Barb, here is a breakdown of my services:

      I’m so sorry you’re going through all of that!

    • Jenny

      Hi Barb! Feel exactly the same as you. I have Graves Disease and in my Thyroid scan and uptake shows my thyroid absorbs 45% iodine so there is a lot “I think” I shouldn’t eat from the autoinmune diet because of the iodine. I’m 35 and have become anorexic and sickly looking.

      Dr. Myers, I’m only taking Glutathione and other supplements yet NO medicine. Following the thirty day protocol of your book, that includes iodine, will it not harm me?

      • Hi Jenny, it completely depends. I can’t really answer that question online, but I would love to see you as a patient so I could help come up with a more specific plan!

  • Alli

    I just finished your book, life changing. I am looking. For the bonus chapter you mentioned…. Where might I find this?

  • Nancy

    Hi Dr. Amy, I read your book, Autoimmune Solutions and have started the diet. I’m a little confused however, about some of the foods to eat or not eat. In the book you say to avoid all dairy, gluten, pseudogluten, nuts, seeds, all sugars with the exception of stevia. I’ve been looking at some of the recipes on your website along with 12 recipes I received by email and these recipes contain honey, flax seed, almond milk, walnuts, & other foods that are to be avoided according to the book. So now I’m wondering what to eat/not eat?

    • Not all of the recipes on my blog are compliant with my autoimmune protocol. Follow the guidelines in the book to be safe!

  • Melody

    hi Dr. Amy,
    I have finished reading your book. I have Hashimotos diagnosed 12 years ago. I have taken b/w .125 and .147 Mg (of Levoxyl depending on my levels) daily. My question is How do you take the supplements on a daily basis, and will they interfere with this med? I have looked for a funct med Md in my area however there are none within 150 goal is to be medication free!!

    • Hi Melody! I hope you achieve that goal 🙂 I can’t really advise about medications unless you come to see me as a patient, but your primary care doctor should be able to tell you whether or not a supplement interferes with your medications!

  • Sharon Ciesla

    Hello Dr. Myers,
    I first listened to your autoimune summit and from there we have instituted GAPS (now full) my 12 y/o with Hashimoto’s (dx 3 mo ago) numbers are now normal but on Levothyroxine 75mcg x6 weeks (dr to decrease at next draw if continues). We have been gluten, dairy, soy free and organic since she was 18 months. We have done candida and parasite cleanses prior to GAPS using Dr Cristophers herbal protocols. My daughter still craves sugar so I am not sure her candida issue is completely resolved. We supplement with fermented cod liver oil, probiotics, zinc, selenium, chlorella, D3 and diatomaceous earth. Homeopath has her on thyroid specific remedies and St. John’s wort. So my question is, will your book give us any NEW insights. From what I have read about your book we are already doing everything you recommend (I think). I realize we have just started on this path to healing and if we just need to stay on course then You can tell us so. Thank you for all your doing for this disorder!!

    • Hi Sharon! Are you able to bring her to see me as a patient? If you really are following the recommendations in my book, a functional medicine practitioner like me could help you figure out the missing pieces! If you aren’t able to come here, you can search for a practitioner in your area:

      • Sharon Ciesla

        Hi Dr. Myers,
        I wish we could come see you, however, we live in Missouri and unfortunately there are no functional medicine drs in our area. I checked within 4 hours of our home 🙁 Thank you,

        Sent from Sharon’s iPhone

      • Sharon Ciesla

        Dr. Myers,
        During the summit you mentioned that you have a water purification system that you like. Do you mind sharing the type of system you are using? Thank you

        Sent from Sharon’s iPhone

  • ChristineL

    Any advice for those of us who cannot manage to go completely grain free? I have tried multiple times, but have been unable to sustain it because I felt so horrible when on a grain free diet. In addition to feeling even worse than before, a completely grain free diet also causes me to have symptoms of interstitial cystitis.

    Also, what about those of us who are using the low FODMAPS diet? This has helped me to an extent. Most of the foods you include in the 30-day plan include high FODMAPS foods such as broccoli, kale, and apples – all of which are severely limited on the low FODMAPS diet.

  • Jenny mccrary

    Please, Dr. Myers, tell some of us who are confused about the the nuts, seeds, almond milk, honey, etc. that we see in your recommended recipes. I had wanted to start the protocol soon but don’t understand the seeming contradiction between what you recommend in your book and your proposed recipes. Many of us have been vegetarians for years, so if chia seeds, nuts, and the like, are not contraindicated, that would be lovely. But if we should not imbibe, we really need to know in order to come up with other possibilities. It is well know that greens are full of proteins and more readily digestible than proteins from meat, so would eating large amounts of them be helpful just in case we could not get used to eating meat? What about protein powders in smoothies? Other possibilities? Would appreciate your help in this matter so very much, as I know others would, also. We do understand how busy you must be, so am not being critical–just wanting full resolution of symptoms as quickly as possible.

    • Hi Jenny, not all of the recipes on my blog are autoimmune protocol friendly, so when in doubt, follow the guidelines in my book. Of course it is going to vary from person to person, but in general I do not recommend nuts and seeds for those with autoimmune disease.

  • christina

    Hello. I just found your website and I’m very intrigued by your approach. I have a question that I just can’t get my Drs to answer. I recently had a blood test and my ANA levels came back very high. I was sent to a Rheumatologist who ran all the standard tests and she sees no signs (either from the test or from the physical exam) of any AID. I know some people just have high ANA, but I just feel “off” and my BM have changed dramatically in the past few months. So, my question is… can food sensitivities contribute to high ANA levels and how does all that relate to systemic inflammation? For the past 45 days i have been completely off all grains, legumes, sugars (all of them), soy, and dairy. And to be honest, I haven’t noticed any changes at all in anything. I”m still tired. My BMs haven’t changed at all.

  • Martha

    Are there any protein powders or recipees that can be used for morning smoothies while following the autoimmune protocol?

  • Mary

    Do any Doctors in Santa Barbara follow the Meyers way to heal

    • Hi Mary, you can search for a functional medicine practitioner in your area here:

      • Mary

        I have looked there and believe it or not Santa Barbara has one and she only sees children. She has no one she recommends. I read somewhere that one endroconoligist read your book here and thought maybe at least they have some interest in finding out what is wrong. Thank you for this wonderful book.

  • Lisa Heins Vincent

    Hi Dr Amy, I am on day 4 of the plan, and I’m wondering if there are any non-salad lunch alternatives. I have gastroparesis, and the high-fat, meat, and raw veggies are exacerbating it. I am committed to staying with the program for the month, but this is making it difficult. Also, any recommendations for constipation?

    • Hi Lisa, many of the lunches on the 30-day program are more than salad. You could also make more food for dinner, and eat the leftovers for lunch. I think the best thing to do would be to set up a consultation with my dietitian, who could come up with a plan that is more specific for you!

  • Cheryl

    Dear Dr. Amy,
    I’m not sure why nuts are part of your elimination diet. Mark Hyman uses nuts in his recipes for his detox an I can’t seem to find where in your book you explain why nuts need to be eliminated. They are ‘healthy’ fat, yes? Do they mimic gluten or some other substance? Thank you! Cheryl

    • My book is for people with autoimmune diseases, and I find that they cause reactions in many people with inflammatory issues. They’re common allergens.

  • Lisa

    Hi, Dr. Myers! I have just started what I hope to be at least 60 days on the Myers Way! I have Inclusion Body Myositis and am determined to beat it! I guess I am already figuring that I will need longer than most. I was diagnosed four years ago, started drinking green smoothies, got rid of GERD and Nexium, Chronic Fatigue Syndrome and Epstein Barr have seemed to disappear, but IBM is still hanging around as well as a low thyroid. I want to do this right! My functional medicine doctor suggested your protocol! Could you please tell me if homemade kefir is still considered dairy on your elimination diet? Also, what about dried apples or other dried fruits with sugar? I have read that kefir was healing for leaky gut, but I want to try to follow your way 100%, so I want to be sure!

    • Yes I still consider kefir a dairy product. I don’t recommend dried fruits while starting out. That’s great that you’ve already come so far! Wishing you the best of health 🙂

  • Julie M

    I would like to start your 30 day plan along with the supplements. I have Hashimoto’s and according to your book I tested positive to having SIBO, yeast overgrowth and a leaky gut. I’ve also been diagnosed with Chronic Fatigue Syndrome. I am a 3rd grade teacher and I struggle with debilitating fatigue and severe depression as well as moderate to severe joint and muscle pain. I would like to begin your plan as soon as possible, however, with the demands of my job along with all these symptoms, my concern is that when I begin the supplements and diet change that the symptoms will get a lot worse making it extremely hard for me to function and get through the day due to die-off, detox, etc. My summer break is 4 weeks away, would it be best to wait and begin the program then?

    • Definitely up to you–some people feel better right away, but some people do have an “adjustment” period. If you are comfortable waiting, it might be best to wait. Stress reduction is a big part of the program! Of course, you could just make a few changes here now, and make some of the bigger changes when you have your break. For example if you wanted to start the meal plan now, I’d say go for it!