The Best Diet to Fix Your Gut Health

Perhaps you have heard of this new diet that recently hit the scene?

The Autoimmune Protocol Diet, or AIP for short, is a relatively new dietary protocol that claims to reduce inflammation, improve immune function, and help manage the symptoms of autoimmune diseases.

Many individuals with autoimmune diseases report that the AIP diet has lessened their disease symptoms, reduced autoimmune flare-ups, and improved their quality of life.

What exactly is the AIP diet, and does the research support this dietary approach for autoimmune disorders?

What is the Autoimmune Protocol Diet?

AIP diet gut health

The Autoimmune Protocol (AIP) diet is an elimination-focused dietary therapy that may help individuals struggling with autoimmune diseases.

Autoimmune diseases are thought to be caused by various risk factors, including genetic predisposition, environmental triggers, stress, systemic inflammation, and certain medications.

Additionally, some preliminary research suggests dietary factors may play a role in the development of these medical conditions among susceptible individuals.

It is hypothesized that certain “trigger foods” may damage the gut wall, which might increase the risk of an autoimmune disorder.

As an elimination diet, AIP involves avoiding these specific foods for several weeks while carefully monitoring disease symptoms and overall health changes.

AIP is rooted in the Paleo diet, although it is considered an even more restrictive diet than the Paleo approach.

Additionally, this diet shares some similarities to a ketogenic diet, as it greatly limits carbohydrate intake.

It includes mostly vegetables (with some exceptions) and animal proteins from meats with the elimination of grains, cereals, legumes, nightshade vegetables, gluten, eggs, dairy, nuts, seeds, coffee, alcohol, refined sugars and sweeteners, and processed foods.

Who Can Benefit From the AIP Diet?

AIP is an autoimmune diet designed to reduce chronic inflammation and help control symptoms of autoimmune conditions.

An autoimmune disease is a condition that develops when your immune system produces antibodies that mistakenly attack the healthy tissues of your own body.

There are over 80 identified autoimmune diseases (1).

Examples include psoriasis, multiple sclerosis, fibromyalgia, eczema, rheumatoid arthritis, lupus, asthma, Hashimoto’s thyroiditis, Shwachman-Diamond syndrome (SDS), and inflammatory bowel disease (IBD), including Chron’s disease and ulcerative colitis (UC) (1).

Common symptoms of autoimmune conditions are fatigue, headache, brain fog, digestion or gut issues, diarrhea, pain, swelling, hair loss, low-grade fever, skin rashes, and stiff or painful joints.

According to the National Institute of Health (NIH), more than 24 million people are affected by autoimmune disorders in the United States (1).

How Does This Diet Work?

While the root cause of autoimmune conditions is not entirely understood, it is thought that complex interactions between genetic predisposition, environmental factors, chronic stress, and the immune system may contribute to the formation of autoimmune diseases and inflammatory diseases (1-3).

Additionally, one hypothesis poses that imbalances in the gut microbiome (aka the healthy gut bacteria) and low-grade inflammation can damage the lining of the intestines.

This imbalance in healthy gut bacteria is sometimes referred to as dysbiosis or gut dysbiosis.

Certain foods are also thought to act as “gut irritants” which cause gut inflammation and irritation and increases intestinal permeability.

This hypothesis suggests that certain autoimmune diseases may be triggered in susceptible individuals, in part, as the result of tiny holes or “leaks” in the intestinal wall, also known as a leaky gut syndrome.

It is thought that these holes may allow gut bacteria, food particles, and digestive enzymes to escape into the bloodstream through the walls of the gut lining in the digestive system.

These leaked materials may then prompt an immune system response. The body treats the leaked particles as potential pathogens or foreign invaders and launches an immune response on its own tissues using antibodies.

This immune system reaction results in widespread, chronic inflammation and further damage to healthy cells and body tissues.

The principle behind the AIP autoimmune diet is that avoiding gut irritants or trigger foods will reduce inflammation and allow mucosal healing of the leaky gut.

Proponents in the AIP community claim that this diet improves the intestinal walls, “fixes” hormones and hormone imbalances, and resets the body’s immune system by identifying and eliminating inflammatory foods that trigger inflammation in the body.

Few studies have investigated leaky gut syndrome; however, researchers agree that certain diseases are associated with greater intestinal wall permeability and impaired gut health (4).

It is important to note that AIP is not a cure for autoimmune diseases. Although conventional medicine aims to lessen autoimmune symptoms and reduce symptom flare-ups, there are currently no cures for autoimmune conditions.

In some cases, periods of symptom remission or clinical remission (when there is no objective evidence of active disease) is also possible.

However, AIP may be used as an adjunctive treatment to help manage autoimmune symptoms, identify food sensitivities, improve gut health, and increase nutrient absorption and metabolism, although further research is needed to support these claims.

Foods to Avoid

The AIP diet is an elimination diet, meaning that certain foods are removed from the menu for 30 days or longer to identify food intolerance.

This autoimmune diet is similar to the Paleo diet, as it excludes processed foods, grains, dairy products, and legumes.

Foods eliminated as part of the AIP diet include:

  • Grains, whole grains, cereals, and gluten, including wheat and rice
  • Legumes, such as peanuts, chickpeas, beans, soy, and lentils
  • Refined carbohydrates (or carbs) and added sugars, such as those found in cookies and cakes
  • Nuts and seeds, including items derived from this food group such as coffee, chocolate, certain vegetable seed oils, and certain spices such as cumin and coriander.
  • Vegetables in the nightshade family, due to their high content of dietary lectins; includes tomatoes, potatoes, peppers, and eggplants.
  • Eggs
  • Dairy products, including milk, cheese, yogurt, butter, and ghee
  • Certain beverages including coffee, alcohol, and soda
  • Processed foods
  • Processed vegetable oils and seed oils (sometimes dubbed “industrial seed oils”)
  • Food additives, flavor additives, and preservatives
  • Artificial sweeteners
  • Foods high in lectins- Lectins are a type of carbohydrate-binding protein found in nearly all foods, with the highest amounts legumes, cereal grains, and nightshade vegetables.
  • Blue-green algae products and supplements, including chlorella and spirulina

Fruits remain a controversial component in the AIP diet. Some protocols recommend eliminating sugar, including fructose- a natural sugar found in fruits.

The paleo autoimmune protocol from the Paleo Way recommends limiting fructose intake to no more than 20 grams per day (5).

This equates to about two servings of fruit, depending on the type.

Fruits higher in fructose include kiwis, raisins, watermelon, bananas, grapes, and apples. Certain berries, such as raspberries and strawberries, are lower in fructose.

The AIP diet also avoids nonsteroidal anti-inflammatory drugs (NSAIDs), including ibuprofen and aspirin.

Be sure to speak with your doctor before stopping an aspirin regimen or discontinuing any medications.

Some strict, autoimmune paleo versions of this diet also recommend limiting salt and sea salt, saturated fats (like those found in red meats), dietary lectins, omega-6 fatty acids, and natural sugars, such as honey and coconut products.

Foods to Eat

The list of foods that you cannot eat on the AIP diet may sound overwhelming at first, but here comes the fun part… the nutritious foods that you can eat!

This specific diet includes various nutrient-dense foods rich in vitamins, nutrients, antioxidants, and minerals.

Be sure to pick up the following foods the next time you grocery shop:

  • Vegetables, except for nightshades
  • Lean and minimally processed meats, such as poultry, fish, seafood, and organic meat
  • Organ meats
  • Certain oils, including olive oil
  • Fermented and probiotic-rich foods that don’t contain dairy products. Examples include kombucha, pickled vegetables, sauerkraut, kimchi, and non-dairy kefir.
  • Sweet potatoes
  • Green smoothie
  • Cassava and cassava flour
  • Arrowroot starch
  • Coconut, coconut oil, coconut milk, and other coconut products
  • Maple syrup and honey, in small amounts
  • Avocado, avocado oil
  • Avocado and greens smoothie
  • Bone broth
  • Herbs and spices, as long as they are not derived from seeds
  • Gelatin from grass-fed beef
  • Animal fats, such as lard
  • Vinegars, including red wine, balsamic, and apple cider vinegar
  • Green teas, black teas, and herbal teas not derived from seeds
  • Fruits, in moderation

Individuals following the AIP diet are encouraged to consume a wide variety of vegetables, emphasizing cruciferous vegetables.

Examples include broccoli, cauliflower, and cabbage.

Additional veggies that you can load your plate with include leafy greens, green beans, onions, mushrooms, celery, kale, beets, and carrots, to name a few.

While technically considered a legume, green beans are generally accepted as part of the AIP diet.

Good quality seafood and shellfish, especially fatty fish, are a staple of any anti-inflammatory diet due to their omega-3 content.

Omega-3 fatty acids are a type of fatty acid involved in regulating the body’s inflammatory response and work to reduce inflammation.

Research has consistently found a connection between higher omega-3 fatty acid intake and reduced inflammation in the body (6, 7).

Additionally, seafood and shellfish are excellent sources of protein and b vitamins.

Foods like salmon, tuna, halibut, and sardines are good sources of zinc, healthy fats, and omega-3s, which are usually lacking in the western diet.

In general, you should aim to consume high-quality seafood at least three times per week for better health.

Honey and maple syrup are controversial components of the AIP diet, with some proponents recommending natural sugars in moderation.

In contrast, others recommend removing added sugars as part of this lifestyle intervention.

Currently, the paleo autoimmune protocol recommends eliminating all-natural sweeteners and artificial sweeteners from the diet, including honey and maple syrup (5).

How Long Should You Follow the AIP Diet

The AIP diet is a type of elimination diet, meaning that you eliminate possible trigger foods for a set number of weeks before gradually adding foods or food groups back into the diet while monitoring for symptoms.

Elimination diets are useful for identifying food sensitivities, intolerance, and allergies.

There are two phases: the elimination phase and the reintroduction phase.
As the name suggests, the elimination phase involves the elimination of foods that may be causing an autoimmune reaction. In general, the typical amount of time spent in the elimination phase is about 4 to 6 weeks.

The next step is the reintroduction phase. This phase aims to identify foods that cause autoimmune symptoms or sensitivities and reintroduce any and all foods that do not result in symptoms back into the diet.

In this phase, eliminated foods or food groups are slowly reintroduced into the diet one at a time over 2 to 3 days to determine the impact of diet on symptoms.

During this time, you can carefully monitor for symptoms of inflammation. Some people may find it useful to keep a food journal or symptom diary during this phase to watch for significant change during food group reintroduction.

Examples of symptoms include skin rashes, joint pain, headaches, fatigue, bloating, arthritis pain, asthma, stomach pain, diarrhea, and digestive problems. Individual diseases may also have their own unique signs or symptoms. For example, someone with active IBD may experience bloating or stomach cramps, while someone with arthritis may notice stiff joints.

A return in symptoms could indicate a food intolerance or sensitivity, and you may consider eliminating that food from your diet.

Some individuals may decide to adopt the autoimmune protocol as part of long-term lifestyle changes due to its nutrient density or because of the overall reduction in autoimmune issues.

However, you may want to consult a registered dietitian, functional medicine practitioner, or qualified health coach if you plan to eliminate many foods from your diet, as this could result in micronutrient and nutritional deficiencies.

Overall, the autoimmune protocol is a tool for identifying dietary changes, lifestyle interventions, or dietary factors that may reduce autoimmune symptoms. It is not meant to be a long-term dietary approach.

What Does the Research Say?

The AIP diet is a relatively new dietary intervention, and much of the science surrounding its benefits remains mostly theoretical or based on anecdotal evidence.

There is currently a lack of large clinical trials evaluating the efficacy of AIP, which makes it difficult to provide concrete recommendations about this dietary modification.

However, new research studies are promising and suggest that AIP protocol may be beneficial for individuals with certain autoimmune diseases, including UC and Hashimoto’s.

One study from 2019 looked at the impact of AIP on disease activity among 15 IBD patients, including a final cohort of 6 Crohn’s disease participants and 9 ulcerative colitis (UC) participants.

There was no control group for this trial. Based on the results, study participants experienced significant changes in autoimmune symptoms and quality of life compared to baseline as early as three weeks after dietary intervention (8).

Similarly, a 2017 study that examined the effect of AIP on IBD patients with active IBD (both Chron’s disease and UC) found that participants had significant improvements in symptoms and stress management following the 6-week dietary elimination and 5-week maintenance phase compared to baseline (9).

A different pilot study involved the enrollment of 16 women with Hashimoto’s thyroiditis, which is an autoimmune disorder that impacts the thyroid gland and can result in hypothyroidism (10).

Study participants followed the AIP protocol for 10 weeks. At the end of the study, inflammatory biomarkers decreased by 29% compared to baseline, and autoimmune symptoms decreased by 68% compared to baseline levels. There were no significant differences or clinical response in thyroid function at study completion (10).

Additionally, research has noted that autoimmune diseases, including food allergies, celiac disease, Crohn’s disease, and ulcerative colitis (UC) are associated with greater gut permeability or porousness (4, 11, 12). However, further research is needed to explore the relationship between leaky gut syndrome and autoimmune diseases.

Although promising, it is important to keep in mind that these studies had limited enrollment and a small sample size.

Additionally, most of these preliminary studies did not have a control group and focused on a small subset of autoimmune conditions, such as IBD or UC. Further clinical trials are needed before conclusions can be made concerning the autoimmune protocol.

Additional Considerations and Possible Adverse Effects 

This autoimmune diet is an elimination diet and is, therefore, a restrictive diet, especially during the elimination phase. The long list of foods not to eat may leave many feeling hungry and with food cravings.

The good news is that the elimination phase is only one part of this anti-inflammatory diet. If you experience no symptoms during the reintroduction of specific food or food groups, then you can incorporate those foods into your diet once again.

However, some individuals may be hesitant or fearful to enter the reintroduction phase, as it may trigger a flare-up of symptoms. Once someone is almost symptom-free or has achieved a form of clinical remission, it may be scary to reintroduce potential trigger foods into their diet.

This is a concern because the AIP protocol is highly restrictive, and remaining in the elimination phase for too long may result in micronutrient deficiencies. Anytime that you remove whole food groups from the diet, there is a chance of nutritional deficiencies.

For example, this anti-inflammatory diet is notably low in calcium, soluble fiber, and vitamin D, to name a few. Additionally, this diet eliminates many healthy foods, including whole grains and legumes, which are a good source of zinc, b vitamins, magnesium, and soluble fiber.

It may be a good idea to seek professional medical advice from a qualified practitioner before starting this protocol. A functional medicine practitioner or registered dietitian can help you better identify food intolerances while making adjustments to your meal plans to ensure nutritional adequacy.

Some people may find this elimination diet has too many restrictions. Individuals with a history of eating disorders may want to seek professional counseling from a practitioner before trying any restrictive diet.

Furthermore, people with multiple food aversions, food allergies, or those who follow a vegan diet may find that this dietary approach does not offer enough variety to meet nutritional needs.

Additionally, it is important to note that there is limited research exploring the efficacy of the AIP diet and the role of diet on autoimmune conditions. Further research is needed to establish a link between AIP and potential clinical remission from an autoimmune disease.

The Final Word

Living with an autoimmune condition presents many health challenges and significantly impairs an individual’s overall health and quality of life.

While there is currently no cure, it is possible to manage the symptoms of an autoimmune disease, and periods of clinical remission is possible in some cases.

Preliminary research on the AIP dietary intervention, while limited, appears to be promising.

Small studies have currently reported benefits among individuals with a health history of IBD, active IBD, and Hashimoto’s thyroiditis.

However, more research is necessary to determine the impact of AIP on other autoimmune diseases, such as eczema, rheumatoid arthritis, lupus, asthma, and Shwachman-Diamond syndrome (SDS).

While further research is needed, this dietary modification may help reduce baseline inflammation and improve the quality of life for the many people struggling with autoimmune diseases.

Theoretically, the AIP autoimmune diet may also help heal a leaky gut. However, clinical trials are needed to support this hypothesis.

Additionally, this diet may encourage individuals to eat more nutritious foods, as it restricts processed foods, refined carbohydrates or carbs, and added sugars while emphasizing meats, lean proteins, veggies, and real foods.

This diet may also help with optimal health, wellness, insulin resistance, and blood sugar control as it requires careful meal plans and can be used as the building blocks for a weight loss program.

However, this protocol is not meant to be a long-term lifestyle modification.

Rather, it is a tool that can help identify food sensitivities and intolerance and may result in nutrient deficiencies if followed for months.

Keep in mind that food choices are not the only way to manage autoimmune disease.

On top of eating a nutrient-dense diet, getting enough sleep and physical activity, stress management, meditation, and quitting smoking are also important lifestyle factors that may help reduce inflammation in the body.

Perhaps the best way to get started is by talking to a healthcare practitioner, registered dietitian, or qualified health coach to determine if this dietary protocol is a good option for you.

  1. “Autoimmune Diseases.” National Institute of Environmental Health Sciences, U.S. Department of Health and Human Services, www.niehs.nih.gov/health/topics/conditions/autoimmune/index.cfm.
  2. Minihane, Anne M et al. “Low-grade inflammation, diet composition and health: current research evidence and its translation.” The British journal of nutrition vol. 114,7 (2015): 999-1012. doi:10.1017/S0007114515002093
  3. Belkaid, Yasmine, and Timothy W Hand. “Role of the microbiota in immunity and inflammation.” Cell vol. 157,1 (2014): 121-41. doi:10.1016/j.cell.2014.03.011
  4. Arrieta, M C et al. “Alterations in intestinal permeability.” Gut vol. 55,10 (2006): 1512-20. doi:10.1136/gut.2005.085373
  5. “Autoimmune Protocol.” The Paleo Way, thepaleoway.com/autoimmune-protocol.
  6. Simopoulos, Artemis P. “Omega-3 fatty acids in inflammation and autoimmune diseases.” Journal of the American College of Nutrition vol. 21,6 (2002): 495-505. doi:10.1080/07315724.2002.10719248
  7. Li, Kelei et al. “Effect of marine-derived n-3 polyunsaturated fatty acids on C-reactive protein, interleukin 6 and tumor necrosis factor α: a meta-analysis.” PloS one vol. 9,2 e88103. 5 Feb. 2014, doi:10.1371/journal.pone.0088103
  8. Chandrasekaran, Anita et al. “An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease.” Crohn’s & colitis 360 vol. 1,3 (2019): otz019. doi:10.1093/crocol/otz019
  9. Konijeti, Gauree G et al. “Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease.” Inflammatory bowel diseases vol. 23,11 (2017): 2054-2060. doi:10.1097/MIB.0000000000001221
  10. Visser, Jeroen et al. “Tight junctions, intestinal permeability, and autoimmunity: celiac disease and type 1 diabetes paradigms.” Annals of the New York Academy of Sciences vol. 1165 (2009): 195-205. doi:10.1111/j.1749-6632.2009.04037.x
  11. Groschwitz, Katherine R, and Simon P Hogan. “Intestinal barrier function: molecular regulation and disease pathogenesis.” The Journal of allergy and clinical immunology vol. 124,1 (2009): 3-20; quiz 21-2. doi:10.1016/j.jaci.2009.05.038

 


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