The Autoimmune Epidemic: Part 3 Autoimmune Protocol


This is part 3 of a three-part blog series covering the ins and outs of autoimmune disorders. Part 1 explained that autoimmune diseases are an unspoken epidemic affecting far more people than is currently realized. In part 2, we discussed the connection between leaky gut, immune system function, and autoimmune disease. In this final article of the series, we will take a closer look at new research demonstrating precisely how diet and gut health are intimately connected to autoimmunity. I will also explain how the Autoimmune Protocol of the Paleo diet can be used to overcome most, if not all autoimmune disorders by facilitating the healing of a leaky gut.

A Leaky Gut Can and Does Trigger Autoimmune Disease

autoimmune-tract2p3-300x171.jpgIn part 2 of this series, I explained how a leaky gut precedes most, if not all autoimmune diseases. Emerging research continues to reveal that a leaky gut can be caused by many different things, but is particularly triggered by imbalances in our gut bacteria (dysbiosis) and by the chemicals found in grains and legumes (especially gluten). Dysbiosis and gluten cause the gut wall to release a molecule called zonulin. In all people, zonulin increases intestinal permeability (leaky gut) by triggering the opening of the tiny gates that connect adjacent cells in the gut wall. (Remember that the gut wall is only one cell layer thick!) These little gates are called ‘tight junctions’, and they are normally closed so tightly that nothing except water and digested nutrients can freely pass through the gut wall. However, in a leaky gut, large particles from inside the gut (like bacteria, viruses, antigens, toxins, and partially-digested food) escape through the open tight junction gates, and into the body.

autoimmune-leaky-gut1-p3-300x225.jpgThere is a reason why nature placed 70-80% of our immune system in and around our gut wall; apparently nature thinks the gut is a pretty dangerous place! If a leaky gut is allowed to persist, the gut’s immune system will eventually become overwhelmed from the massive influx of toxins. At this point, the contents of the gut (that the body would normally never be exposed to), can gain access to the bloodstream. Once in circulation, the toxins can travel to virtually any location in the body, and initiate an inflammatory immune response wherever they land. The destruction that ensues is known as autoimmune disease.

New Theory of Autoimmune Disease: A Trio of Triggersautoimmune-triggers-p3-241x300.jpg

A growing body of evidence inspired by the discovery of zonulin suggests that a trio of factors underlies most, if not all autoimmune diseases. Dr. Alessio Fasano (the researcher who discovered zonulin) has proposed that three factors must be simultaneously present for autoimmune diseases to be active in the body. According to this most recent theory of autoimmune disease, if only one factor of the trio is removed, an autoimmune disease will go into remission.

The trio of requirements for autoimmune disease(s) to be active include:

1. A genetic predisposition to autoimmunity, such as those people who carry the HLA gene (a gene that predisposes a person to developing autoimmune disease)

2. A leaky gut (caused by zonulin)

3. Environmental triggers that are causing the release of zonulin from the gut wall (i.e. gluten, grains, legumes, bacterial overgrowth, etc.)

autoimmune-tip-p31-300x225.jpgBy this theory, all autoimmune diseases can be stopped or reversed if at least one of these three factors is removed. We can obviously not remove our genetic predisposition to autoimmune disease (at least not yet). However, we can very much remove the second and third factors by healing our leaky gut. As explained in part 2, several different triggers can induce leaky gut via the release of zonulin from the gut wall, but the chemicals found in grains (especially gluten) as well as an unbalanced gut microflora (dysbiosis) are some of the most potent causes of a leaky gut.

Why Plants Don’t Want You to Eat Their Babies

autoimmune-antinutrient-p31-300x294.jpgIn most people suffering from autoimmune disease, going ‘gluten-free’ is often not enough to put their condition into remission if they are still consuming other grains and legumes. Indeed the complete removal of grains and legumes is often required to completely heal a leaky gut. Grains and legumes are seeds, and all seeds can be viewed as the babies of plants. Just like all mothers, the plant wants more than anything to keep its babies alive, to ultimately ensure the survival of its species. That is why plants concentrate chemicals (collectively referred to as antinutrients) in their seed babies. The antinutrient chemicals in seeds are lethal to bugs, bacteria, and other small critters that really want to eat the nutrient-dense seed. In larger mammals, the antinutrients are generally not lethal (at least not immediately), but they do cause irritation to the gut lining, and can eventually result in leaky gut syndrome. Among the various seeds, the grains and legumes are some of the worst when it comes to irritating the gut lining and instigating a leaky gut.

Heal Your Leaky Gut to Overcome Autoimmunity

Some goals to keep in mind when you are changing your diet to overcome autoimmunity are

autoimmune-irritants-p3-300x272.jpg1. Heal the leaky gut by removing irritating foods that are causing the leaky gut in the first place. This is where the autoimmune protocol (AIP) of the Paleo diet can be really helpful.

autoimmune-flora-p3-206x300.jpg2. Heal the leaky gut by addressing gut flora imbalances (dysbiosis) and strive to attain a healthy gut microflora (orthobiosis). This may involve keeping sugar/carb intake low and rotating the plant fibers in the diet. Probiotics or prebiotics may also be needed, and it can be helpful to work with a health care provider who specializes in restoring orthobiosis, as this is a highly individualized endeavor.

autoimmune-stress-p3-300x199.jpg3. Stress is also a potent trigger of leaky gut. I’ve had re-flares of my autoimmunity just by getting too ‘stressed out’ and I’ve had to learn ways to manage my stress levels through meditation, deep breathing, exercising, time management, and getting enough sleep consistently. In addition, many autoimmune diseases are initially triggered by a stressful event, like an illness or the death of a loved one. It’s important that we learn to minimize negative stress wherever we can, and to learn stress-management skills to best handle the inevitable stressors that will occur in life.

autoimmune-time-p3-300x211.jpg4. Time is of the essence. In my experience, the more ‘comfortable’ a disease gets in your body, the more difficult it is to eradicate. With autoimmune diseases, the tissue destruction that results from active ‘flares’ can create permanent damage that may not be able to be healed by diet alone. As yourself: is there a good reason to wait any longer?

The Autoimmune Protocol (AIP) of the Paleo Diet

autoimmune-protocol-p3-280x300.jpgA rapidly growing number of individuals (myself included!) have been able to put our autoimmune diseases into remission by following the autoimmune protocol (AIP) of the Paleo diet until the leaky gut is healed. It stands to reason that if a person is plagued with autoimmunity, then their gut is probably quite leaky and in need of some serious healing. To heal a leaky gut takes most people several weeks, months, or even years to accomplish. While this may sound difficult, I encourage you that it is waaaaaaaaay easier than suffering from the pain that will result from the destruction of your own body by autoimmune disease.

The AIP of the Paleo diet is similar to the standard Paleo diet in that it involves the removal of all grains, legumes, dairy, most sweeteners, vegetable oils, and other processed foods and drinks. The AIP takes things a few steps further by also eliminating the following foods (at least initially…and ideally until a person achieves remission from their autoimmunity):

  • Eggs (especially the white part of the egg that contains inflammatory proteins)
  • All nuts and seeds (these also contain gut-irritating antinutrients)
  • Anything derived from a nut, seed, grain, or legume (coffee beans, cocoa beans (chocolate), seed-based spices, nut flours, etc.)
  • Nightshades (This is a family of plants containing various chemicals known to cause leaky gut. Some nightshade plants include tomatoes, all peppers, potatoes, tomatillos, paprika, goji berries, eggplants, and others.)
  • Alcohol (well known cause of leaky gut syndrome)
  • NSAIDs (Non-steroidal anti-inflammatory drugs such as Ibuprofen, aspirin, and naproxen, which are also well-documented to wear away at the gut and stomach lining)
  • Gluten cross-reacting foods (Some foods can trick the body into thinking that you’re eating gluten, such as coffee, fermented foods, yeast-containing foods, chocolate, etc.)
  • Sugar, starches, fruits, FODMAPs (These sweets can contribute to dysbiosis by feeding unfavorable bacteria in the gut. They are best limited or restricted especially at first on the AIP).

Ask Yourself: Is It Worth It?

autoimmune-healthy-path-p3-300x262.jpgOk I know what you must be thinking: the autoimmune protocol sounds scary! I totally hear that. The thought of letting go of something that you love, depend on daily, and are quite possibly totally addicted to, sounds downright terrifying. It is truly a loss of great magnitude that can elicit similar feelings to going through a horrible break-up. So if you simply cannot fathom the thought of giving up certain foods, even for a MONTH to see if they are contributing to your autoimmunity, then I suggest taking baby steps and eliminating one or two foods at a time. I should warn you, that it will likely take a lot longer to heal your leaky gut this way.

The other option is to just go full-on AIP diet from day one, and get all of the grieving of loss and ‘detoxing’ accomplished all at once (instead of spreading it out over several months). It will likely be a tough first month, but this method will achieve the most rapid and drastic results for your autoimmune disease. After being strict Paleo for a few months, my autoimmunity had largely gone into remission, but I was still experiencing occasional flares. I decided to transition to the AIP, which I followed for about 9 months before one day I realized that I couldn’t remember the last time I’d had a flare. How cool is that?!? I then made the bold decision to SLOWLY reintroduce foods back into my diet, which has been largely successful. I now eat a Paleo/primal diet, and strictly avoid all grains, legumes, seed/vegetable oils, and processed foods. Eating out at restaurants almost always makes me sickautoimmune-kinsey-p3-300x225.jpg (because of the crappy oils they use). If I over-consume any of the foods on the AIP, then I experience a re-flare of my symptoms, so I am highly motivated to frequently rotate my foods and to not eat too many nightshades, nuts, seeds, chocolate, etc. in any given sitting, day, or week. I’ve used food as my medicine, and I feel very blessed to have been able to overcome my multiple autoimmune diseases without the use of prescription medications, simply by changing my diet and lifestyle.

Putting the Pieces Together

autoimmune-solution-p3-300x200.jpgI would like to conclude this 3-part blog series by sincerely thanking you for taking the time to read this information, which I know can be difficult for some people to hear. Our current theories of autoimmune disease will keep evolving as researchers continue to define the precise mechanisms involved in autoimmunity. We know so much more now than we did 10 years ago, and the solution is finally within our reach. To summarize, here are some of the main points that I think are critical to understand if you feel ready to take the bull by the horns, and overcome your autoimmune disease.

  • Autoimmune disease is an unspoken epidemic that’s believed to affect around 10% of people, and occurs to some degree in everyone.
  • Leaky gut lies at the root of most, if not all autoimmune diseases.
  • Leaky gut is triggered by grains, legumes, and other gut-irritating foods.
  • Leaky gut also results from imbalanced gut flora, which is called dysbiosis.
  • We now have scientific evidence that demonstrates precisely how leaky gut causes autoimmune diseases via the production of a molecule called zonulin.
  • The most current theory of autoimmunity explains that three factors must simultaneously be present in order for autoimmune diseases to be active: genetic predisposition, a leaky gut, and trigger(s) for the leaky gut.
  • Healing your leaky gut will quite possibly put your autoimmune disease into remission.
  • The Paleo diet may be enough to keep your autoimmune disease in remission, but most people need to be more strict at first by following the AIP (or a similar gut-healing protocol) to fully heal their leaky gut.
  • If you have an autoimmune disease, you will probably need to avoid eating grains, legumes, and other foods that trigger your leaky gut for the rest of your life.
  • While this may all sound difficult to do, it is far less difficult than the inevitable destruction that will result from your own immune system destroying your body.
  • If you are confused about where to go from here, we’ve created a 21 day cleanse that will help you to get started down the road to recovery.

If you’ve kept up with me through part 1 and part 2 of this  3-part blog series covering our current autoimmune epidemic, it probably won’t surprise you when I tell you that leaky gut syndrome has been correlated with many more diseases in addition to autoimmune diseases. Groundbreaking research has also connected  leaky gut syndrome with a long list of maladies including multiple types of cancers, neuroinflammatory diseases (i.e. depression and other psychological disorders), and several other intra- and extra-intestinal pathologies, many of which now have a zonulin biomarker. The realization that a leaky gut lies at the root of many diseases and disorders is not new;  it is something that humans have understood since antiquity. Unfortunately, our modern era of medicine requires “scientific proof” which often takes a long time to be put into practice and recommended to the masses. It has taken researchers a long time to finally catch up with what we have long known: that gut health is a lot more important than we are made to realize. As the Father of Western Medicine (Hippocrates) told us over 2,000 years ago:

autoimmune-free-p3-300x300.jpg“All disease begins in the gut.”
“Let food be thy medicine, and medicine be thy food.”
“Natural forces within us are the true healers of disease.”

I truly wish you the best of luck and urge you to stay strong as you summon your inner forces, and take command of your health, one gut-healing bite at a time.


In good health,
Kinsey Jackson, CN, MS, CNS®


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