Why Aren’t My AIP Reintroductions Working?

The Autoimmune Paleo diet is becoming the go-to first approach to treating autoimmune disease, and rightly so. As a Certified AIP Coach, Naturopathic Doctor and Functional Medicine Practitioner, I have witnessed clients with widely varying autoimmune conditions see incredible improvement after implementing the protocol.

However, one of the biggest concerns I see in clinical practice is the inability to introduce foods back into the diet after the elimination phase. Research has shown that staying on a restrictive diet long-term, where entire groups of food are eliminated, is counter-productive to health and can negatively impact your gut microflora.

So, does that mean that the autoimmune protocol is a bad thing? Absolutely not! Most likely the gut issues were there long before you made diet changes, however, when starting a new diet or making changes to the foods you eat, especially restricting food groups, this will impact the diversity of your microflora. Unfortunately, this can lead to challenges when reintroductions begin and it might feel like nothing is working, or that you’re suddenly reacting to everything.

The common reason some reintroductions don’t seem to work? The gut.

It has been said for years that good health starts in the gut. With emerging research, that is also ringing true for autoimmunity, and in the last 10 years research has linked leaky gut syndrome (or intestinal permeability) to be the leading condition that causes autoimmunity. The question then is, what could be causing leaky gut syndrome and why isn’t it resolving if we’re using the autoimmune protocol to clean up our diet and lifestyle? While the AIP diet is one of the quickest ways to reduce inflammation and calm the immune response, for some it just isn’t enough. Let’s dive deeper into why this might be.

We have over 40,000 different species of microbes in and on our body, with the gut providing the most diverse and dense population of bacteria. Did you know our gut microbiome actually has more biodiversity than a rainforest? [1] We all know that not all bacteria is bad, many are essential to our health and have been shown to prime our immune system in our early years, regulate immune function as we age, and they are even capable of turning on and off our genes, which can make us more susceptible to disease if our microbial diversity is out of balance.

Research is showing that balance and location of the bacteria is the key to a healthy gut. Not all pathogenic bacteria like E. coli are are 100% bad, they actually help stimulate gut lining regeneration, however, once overgrown and in the small intestine they are problematic. [2]

Research has linked pathogenic or opportunistic bacterial that is out of balance and in the wrong location as a trigger to several autoimmune conditions such as RA, MS, DMT1, IBD and now Lupus. [3, 4, 5]

In general, research is indicating that there are 4 key areas of gut health associated with autoimmune conditions:

  1. Pathogenic bacterial imbalance (dysbiosis) has been shown to be present in several autoimmune conditions
  2. Lack of beneficial bacteria populations
  3. Lack of beneficial bacterial diversity
  4. Loss of tolerance to self due to molecular mimicry (immune system can’t tell the difference between our own cells and bacteria)

Why is pathogenic gut bacteria a problem for autoimmune disease?

Why is this a problem? Because pathogenic bacteria produce toxins, cause inflammation and further trigger the immune response. Let’s look at this in more detail:

  • Pathogenic gut bacteria create some of the most toxic material. Lipopolysaccharides (LPS) are found on the cell wall of many bacteria and are released into the gut, accelerating a leaky gut situation, causing further inflammation, immune triggers, and extra stress on liver function.
  • The digestive tract has its own immune system. IgA reactions (or food sensitivity reactions) are a first defense, but for many of us this state of dysbiosis may have been occurring for years, leading to exhausting the first line of defense, leaving you exposed or calling for stronger immune response, which creates more damage and destruction.
  • Over-population of pathogenic bacteria could also mean a lower level of the beneficial bacteria which has been shown to be protective and have anti-inflammatory properties.
  • Pathogenic bacteria could be the driver for leaky gut, altering the intestinal barrier, allowing the pathogenic contents to easily pass through.

What are some of the clinical symptoms you can look for that might indicate bacterial imbalance or dysbiosis?

  • Gas
  • Bloating
  • Heartburn, indigestion or GERD
  • Burping or the feeling of relief after burping
  • Foul smelling gas or stool
  • Diarrhea or constipation
  • Chronic low iron despite eating red meat
  • Feeling worse after eating foods higher in carbs or sugars (even healthy foods)
  • Still hungry after eating a large meal of vegetables and proteins
  • Cravings of sweets
  • Reaction to fermented foods

If you’re finding the reintroduction of foods a challenge, you feel like you’re reacting to everything or feel the need to remove more foods from your diet, it’s time to listen to your gut and get help!

Test, Don’t Guess!

Testing is encouraged because there could be other causes that are not linked to gut flora, such as low stomach acid, hormone imbalances and high levels of stress (cortisol/adrenaline) — all of these things impact gut function and create a leaky gut.

If you suspect that you might have dysbiosis, there is testing that can help determine this. Knowing which pathogenic bacteria are present, determining levels of good bacteria and exploring other habits makes it easier to treat with either herbs or pharmaceuticals.

Types of tests that can be useful:

  • Bloodwork — elevated or lower white blood cell count could indicate the immune system has been trying to fight off an infection or virus.
  • Comprehensive stool analysis — the big picture, and will help you determine overall digestive function (enzyme and fat breakdown), inflammatory markers, levels of good and bad bacteria.
  • SIBO (small intestine bacterial overgrowth) — will reveal if you have bacteria present in the small intestines by measuring the methane, hydrogen and in some of the new tests, sulphur.
  • H. Pylori is the common pathogenic bacteria in the stomach — testing options are breath, stool and blood.

How can you start correcting gut dysbiosis?

  • Probiotics and fermented foods are important for creating and feeding the good bacteria, provided that they are dairy-free (make sure it’s indicated on the label). However, if you find fermented foods or probiotics reactive and feel worse this could be a big sign that you have dysbiosis.
  • Herbs such as oregano oil, garlic, olive leaf and goldenseal have been clinically shown to have antimicrobial properties.
    • *Caution these may also deplete the good bacteria as well. I recommend seeking the advice of a professional to determine which herbs and doses are effective for the bacteria you’re dealing with.
  • Fish oil has been shown to improve the diversity of good bacteria.
  • Diversify your diet! Ensure you are feeding the good bacteria. Research has shown that moving towards a diet high in vegetables and fruit (mediterranean style diet) increases the diversity of the gut flora after just 4 months. This is the opposite of a long-term restrictive diet which might feel good but may not solve the problem.
  • Check your oral health. Regular check-ups, brushing and flossing can prevent bacterial infections. In a large study done in the US, subjects with rheumatoid arthritis were more likely to have periodontitis vs the non-RA controls. One of the top infections linked to RA is gingivitis caused by P. gingivalis and other bacteria found in the mouth. [4]
  • Keep the bowels moving! One of the biggest causes of small intestine bacterial overgrowth (SIBO) is constipation. However, one of the top reasons for constipation is bacterial imbalance (dysbiosis). Magnesium citrate, malate or glycinate are all beneficial for moving the bowels, as is ensuring you’re drinking enough water and eating enough fibre (veggies) daily.
  • Optimize meal frequency. Having a 2-3 hour break between meals allows digestion to run to completion, ensuring the migratory motor complex (which is a wave that clears out bacteria of the small intestines) to operate. Eating frequently or grazing actually turns off this function, putting you at high risk for SIBO.
  • ​​Spend more time outdoors. This has been shown to increase gut diversity plus you have the added bonus of stress reduction. [6]

The causes of autoimmune disease are multifactorial. Diet has a very important part to play in healing, not only because of food sensitivities triggering the immune and inflammatory response, but also because it feeds good or bad bacteria and either supports or destroys the digestive tract. If you’re struggling to reintroduce foods back into your diet consider investigating your gut flora, it could be the missing link. For more information on digestive health and autoimmunity check out my podcast, Autoimmune Simplified or visit www.AlisonDanby.com or www.theautoimmuneclinic.com.


  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577372/
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510460/
  3. Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal Doua Azzouz,1 Aidana Omarbekova,1 Adriana Heguy,2 Dominik Schwudke,3 Nicolas Gisch, 3 Brad H Rovin,4 Roberto Caricchio,5 Jill P Buyon,1 Alexander V Alekseyenko,6 Gregg J Silverman 1 (https://ard.bmj.com/content/annrheumdis/78/7/947.full.pdf)
  4. https://pubmed.ncbi.nlm.nih.gov/18050377/
  5. https://pubmed.ncbi.nlm.nih.gov/10342649/
  6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5744394/

About Dr. Alison Danby

Dr. Alison Danby is a Naturopathic Doctor and Functional Medicine Practitioner who has a focus on autoimmune conditions. She is the founder of The Autoimmune Institute, The Autoimmune Integrative Clinic and owner of The Root of Health, Integrative Health Clinic. Dr. Danby's mission is to change the paradigm of how we medically treat autoimmune disease. She works with clients to find out why the immune system is overreacting and piece together their health puzzle. In order to calm the immune system, we need to identify why it’s over-stimulated and what is triggering it. When we remove the triggers, we allow the body to start the healing process. Without this step, it can be a lifelong challenge of chasing symptoms with medication.


  • Ashley Conboy says

    So I did AIp over 6 years ago. I’ve done so many tests the ig(A) igG tests showed a ton of foods I was able to tolerate, all of which caused insane reactions I have worked with so many do tees and spent so much money and I am still limited to about 15 foods or less and very few fruits and veggies I can tolerate I can tolerate only fish for protein and grass fed steak in extremely small doses. I can’t have bone broth or any collagen no eggs nuts seeds, I can only juice greens and otherwise don’t tolerate any veggies besides cucumber, I no longer tolerate avocado banana, apple, oranges (basically berries and pineapple are all) It’s been extremely hard and as a mom of 6 I can’t continue to reintroduce or spend money… ideas?

    • Mickey Trescott says

      Hi Ashley! I’m sorry to hear you are struggling so much with this. We aren’t huge fans of food sensitivity testing as they often come up with many foods when a person has a leaky gut, and lead to an unnecessarily restricted diet. My recommendation is to find a healthcare provider who is familiar with AIP who can help guide you through this process. We have a long list (including Dr. Danby who wrote this article!) at http://aipcertified.com/coach-directory. Good luck!

  • Janet says

    Thanks for the article. I have Graves disease and Eosinophilic esophagitis. After 8 week elimination diet, I am having trouble re-introducing eggs, something I was always ok with and muscle testing approved them. Now I have canker sores and a sore, raw tongue. Everything I eat burns! This is really depressing me and I don’t know what to do.

    • Mickey Trescott says

      Janet, if you are experiencing symptoms after eating eggs, it might be a sign that you don’t tolerate them. Unfortunately they are a very common sensitivity. If you feel like you want to do some exploring to see if an underlying gut issue might be a root cause, I highly recommend seeking out a functional medicine provider like Dr. Danby who can help you out.

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