Energy Nutrition is the Key to Healing Autoimmune Disorders

Energy is the core of who we are. And it’s the key to healing our most tenacious and painful disorders: autoimmune inflammatory diseases.

There are four core issues that contribute to the perfect storm of autoimmune disorders and their suffering:

  1. genetic susceptibility,
  2. impaired intestinal permeability and microbiome imbalances,
  3. an immunological “trigger” (or multiple triggers), and
  4. energy deficit.

Genetic Susceptibility

The genetic susceptibility piece is hard to predict, poorly understood, and likely present in all of us to varying degrees and at different stages of our lives. We know through the science of epigenetics that genetic expression can be changed through the influence of an infinite array and interaction of environmental and lifestyle factors. This puts all of us at risk for autoimmunity in the “right” circumstances.

Impaired Intestinal Permeability and Microbiome Imbalances

Impaired intestinal permeability is a product of our toxic world, medications, suboptimal lifestyle factors, and gut microbiome imbalances that injure and irritate the gut. We’ll discuss the role of this in autoimmunity in an upcoming section.

Immunological Triggers

Immunological triggers are common and hard to predict when they become significant enough to generate autoimmunity. Everything from emotional stress, trauma, to severe or persistent infections and allergies have been implicated in the genesis of autoimmune disorders.

Energy Deficit

Energy deficit is present in autoimmunity as both a potential trigger as well as a manifestation of the widespread damage to the Brain-Thyroid-Adrenal-Mitochondrial (BTAM) energy operating system caused by the inflammatory-autoimmune process. It is a feed-forward problem that accelerates and exacerbates the damage and suffering and must be addressed for healing to occur.

Where Do We Start to Heal?

This sounds complicated! So, where do we start the healing?

You guessed it! We start with optimal energy nutrition.

The Functions of Optimal Energy Nutrition in Autoimmunity

  • repair and support of the BTAM energy operating system,
  • repair of the intestinal lining to restore normal permeability,
  • restoration of normal gut microbiome,
  • downregulation of inflammation and autoimmune activity through shifts in genetic expression, and
  • removal of many common immunological triggers.

The Gut-Immune Restoration Intensive Nutrition (GRIN) Food Plan

The Gut-Immune Restoration Intensive Nutrition (GRIN) food plan is designed to help heal those whose chronic fatigue is part of a persistent inflammatory or autoimmune condition and take their healing to a deeper level.

The GRIN food plan is an extension of the Foundational Intensive Nutrition Energy (FINE) food plan, going a bit further by excluding additional food groups that are common irritants to the gut lining (thereby increasing intestinal permeability—see discussion below), as well as triggers for inflammation and toxicity.

GRIN provides foundational gut-immune-nutritional healing that leads to improvement in biological energy, with resolution of chronic fatigue and the constellation of problems arising from the energy deficit.

Who Needs to Follow the GRIN Autoimmune Energy Nutrition Food Plan?

This plan should be considered for anyone with persistent gut or inflammatory-autoimmune disorders who do not achieve optimal healing with the Foundational Intensive Nutrition Energy (FINE) Food Plan.

Chronic Autoimmune Disorders that Respond beautifully to GRIN:

  • rheumatoid arthritis,
  • lupus,
  • Hashimoto’s thyroiditis,
  • celiac disease,
  • multiple sclerosis,
  • inflammatory bowel disease,
  • ankylosing spondylitis,
  • psoriasis, as well as others.

Autoimmunity Can Be Hidden

The GRIN food plan may also be appropriate for people with chronic disease or dysfunction without an obvious inflammatory component who fail to recover with less aggressive approaches.

Often inflammation is covert, without a readily recognized presentation, but may still be a factor. I see this in my practice frequently with people who have fatigue, chronic mood or cognitive dysfunction, or difficulty losing weight. They don’t have sore joints or other signs of overt irritation in their bodies, but we know that inflammation can be a “hidden” player in these issues that respond well to gut-healing, anti-inflammatory approaches to healing.

How the GRIN Food Plan Works: Restoration of Normal Gut Permeability, the Microbiome, and Immune Function

A central theme to chronic inflammatory and autoimmune disorders is impairment of the gut lining that leads to increased gut permeability (“leaky gut”). This problem inevitably leads to an increase in immune cell responsiveness to food proteins, gut microbes, and toxins. It leads to increased transfer of gut-derived or ingested toxins out of the gut and into the systemic circulation, engendering additional immune activation and inflammation.

A normal gut, some thirty feet long from mouth to anus, and the surface area of ten tennis courts, provides us with a very tightly controlled interface between the inside and outside worlds. As you can imagine, just as our skin is a crucial barrier for keeping the outside world out, the gut lining is designed to protect us from all potential threats, while at the same time selectively allowing in nutrients the body needs.

As vast as the gut interface is, the body must contribute more than seventy percent of its immune cells to stand guard along its borders. If the barrier is breached, there is an instantaneous response by immune cells. That response is quite complex and involves a direct attack to the offender as well as chemical signaling to other immune cells throughout the body, inviting them to participate in the protective response. This rapidly becomes a full-body process, amplifying protection as well as potentially spreading havoc from the gut to tissues throughout the body, as far away as the brain.

The gut lining damage that is a foundational part of systemic inflammatory-autoimmune disorders arises from many potential stressors and irritants to the gut. The susceptibility to injury varies from one person to the next.

Common Gut Lining Irritants and Stressors:

  • anti-inflammatory drugs such as Ibuprofen, Aleve, aspirin, and steroids
  • antibiotics
  • alcohol
  • acid-blocking drugs (like proton pump inhibitors and H2 blockers)
  • heavy metals (from environmental contamination, contaminated food, dental mercury amalgams)
  • infections (bacteria, parasites, fungi, viruses)
  • food proteins
  • excessive exercise
  • excesses of stress
  • persistent insomnia or suboptimal sleep
  • nutrient deficiencies and nutrient-poor diets
  • microbiome imbalances

Current scientific thinking is that a key aspect of initiating and perpetuating chronic inflammatory and autoimmune disorders is activation of the immune response when the normal gut barrier, which includes the microbiome, is compromised in a genetically susceptible person.

Exposure of the immune cells that line the gut to ingested food components and toxins results in immune activation that begins and sustains the process.

To heal chronic inflammatory and autoimmune disorders we must heal the gut, restore normal gut permeability, and restore a healthier and more diverse microbiome.

Gut Healing Strategy in Autoimmunity

  • repairing the gut lining through targeted nutrition;
  • removal of all toxins and irritants;
  • restoring normal digestion and absorption of nutrients;
  • restoring the microbiome with probiotics, fermented foods, and prebiotic food;
  • decreasing immune system responsiveness through food modulation and intensive targeted nutrition; and
  • Improve BTAM energy operating system function through energy nutrition.

This comprehensive gut healing effort, when combined with other approaches to reduce physical stress and restore immune balance, will lead to improvement and sustainable resolution of symptoms at a root cause level. The process involves many steps. Food is where we start.

GRIN Is Not Meant to Be a Lifelong Plan

The GRIN food plan is designed to heal your gut, remove the common triggers for inflammation, intensify nutrition, support energy production by the BTAM energy operating system, and reverse systemic symptoms related to gut-immune dysfunction and nutrient deficiencies.

GRIN is not meant to be a lifelong eating strategy.

The vast majority of people use this plan to heal, then are able to successfully reintroduce food groups into their diet without a recurrence of symptoms.

When working with clients one-on-one, I make personalized recommendations depending on how sick they’ve been and what their preferences are. It can be very helpful to have the support and experienced guidance from a Functional Medicine practitioner or functional nutrition professional. However, many people successfully navigate this journey on their own.

The Gut-Immune Intensive Nutrition (GRIN) Food Plan Details

The foundation for the GRIN food plan is FINE. We will be modifying that plan by excluding additional food groups that act as irritants to the gut and immune system.

Recall the Foods to Exclude in the Foundational Intensive Nutrition Energy (FINE) Food Plan:

  • All grains and grain-based products;
  • All animal milk products;
  • All processed, synthetic foods, preservatives, and additives;
  • Unhealthy meats;
  • Excesses of sugar;
  • Artificial and non-nutritive sweeteners;
  • Unhealthy fats.

Recall the Foods to Include in FINE:

  • Healthy meat choices, eggs, and fish;
  • Non-starchy vegetables;
  • Low sugar content fruit;
  • Nuts and seeds;
  • Bone broth;
  • Spices, condiments, food supplements;
  • Healthy fats
  • Beans and legumes;
  • Teas;
  • Fermented foods;
  • Fluids;
  • Smoothies;
  • Appropriate nutritional supplements.

Additional Foods to Avoid on Your GRIN Food Plan

Follow all guidelines for foods to avoid listed under the FINE food plan.

In addition, you will need to exclude the following foods and food groups: (But, remember, this food plan is not about deprivation—though it may feel like that right now—it’s about substitution. Eat as much as you like, just of the good stuff.)


Proteins contained in both the whites and yolks of eggs are common immunological triggers, commonly seen in the setting of impaired gut permeability. Avoid using eggs and all egg-containing products.

Beans and Legumes

This includes all beans, legumes (such as lentils and other dals), and dried peas. These contain abundant lectins on their surfaces, defense molecules that are known to trigger immune cells, resulting in inflammation and gut lining injury.


Nightshades are sources of alkaloids, plant defense molecules that can injure the gut lining. Avoid all white potatoes, tomatoes and tomato products, eggplants, sweet bell peppers (all colors), hot peppers, cayenne pepper, goji berries, paprika, pimentos, tomatillos and some curry powders (check ingredients!). Ashwagandha, an herb commonly contained in adrenal support formulas, is also a nightshade, so look at your supplements carefully.

Note: sweet potatoes and yams are fine to eat.


Avoid all nuts and nut-derived oils. This includes almonds, walnuts, cashews, pecans, Brazil nuts, pine nuts, hazelnuts, and pistachios, along with all nut oils, flours, butters, and milks.


Alcohol is always a gut lining irritant and detoxification challenge in spite of evidence that it is health promoting when consumed in moderation. Avoid all alcohol in beverages as well as cooking during this initial intense phase of the food plan. Moderate alcohol consumption may be added later for many individuals.


Seeds contain protease inhibitors, digestive enzyme inhibitors that keep seeds intact when ingested by animals in the wild. It has been hypothesized that seeds may contribute to maldigestion and gut lining irritation.

In my experience, seeds seldom result in true food sensitivity, and are typically eaten in quantities small enough that the protease inhibitors do not present a problem. I generally allow them in the GRIN food plan but recommend removing them if sufficient healing and symptomatic progress is not made otherwise.

Most Protein Supplements

The only commercially available protein supplements allowed during this intensive phase of your GRIN food plan are gelatin and collagen derived from grass-fed beef, hemp seeds, and other seed-derived proteins (if allowed).

I like the hydrolyzed collagen from Great Lakes Gelatin. It is odorless, tasteless, and performs extremely well, dissolving completely in any liquid at any temperature. It can be added to veggie smoothies, soups, stews, bone broth, and all liquids you wish to consume.

GRIN Strategy for Reintroduction of Foods

As I said, GRIN is not meant to be a lifelong food plan.

We want to put out the fire of inflammation and heal the gut.

We want to build tolerance to foods and create resilience.

Once healed, many people are able to put food groups back into their diets without recurrence of symptoms. For the purpose of optimal nutrition, we’d like to diversify foods in the daily diet.

Following are some simple guidelines for food reintroduction.

Strictly adhere to the GRIN food plan guidelines for at least three months. Your body needs this time to remove immunological debris, heal damaged tissue, restore normal gut permeability, reestablish a healthy gut flora, and decrease the overall responsiveness to culprit foods.

Keep a detailed daily log of food and symptoms.

If your symptoms are not resolved by three months, keep going with the strict GRIN food plan and consult with a Functional Medicine professional.

If your symptoms have resolved, choose the foods you would like to reintroduce first—do not plan to reintroduce gluten or animal milk products initially, or other foods you know for certain have caused you significant problems in the past.

Start with Just One Food at a Time:

  • Have one healthy serving (one-half to one cup) of a pure form of the food you are reintroducing, for example one half cup of almonds or one cup of a nightshade vegetable.
  • Do not eat more of your chosen foods (or other foods on your forbidden list) for three days as you carefully observe for symptoms that may be related to the introduced food.
  • If you feel well, try it a second time, and this time eat one serving per day for a week, while not introducing any other foods you’ve been avoiding on GRIN. This will allow you to discover if your sensitivity to this food occurs gradually with repeated exposures. If all goes well, feel free to add this particular food back to your diet, but don’t eat it every day (increases the risk of re-sensitizing to it). Instead plan to include it on a rotational basis every three to four days.
  • If a food makes you feel unwell at any time during this process, stop eating it and strictly exclude it from your diet.
  • Once you’ve finished exploring your first food, move on to a second in the same careful fashion. If you go too fast, you may end up with symptoms and not know which food caused them, necessitating going back to strict GRIN eating and starting this process over.


Qinghui Mu, et al. Leaky Gut as a Danger Signal for Autoimmune Diseases. Front Immunol. 2017; 8: 598.

Leila Abdelhamid and Xin M Luo. Retinoic Acid, Leaky Gut, and Autoimmune Diseases. Nutrients. 2018 Aug; 10(8): 1016.

Fasano A. Leaky Gut and Autoimmune Diseases. Clin Rev Allergy Immunol. 2012 Feb; 42(1): 71-8.

Silvio M Vieira, et al. Diet, Microbiota and Autoimmune Diseases. Lupus. 2014 May; 23(6): 518-526.

Andrew W Campbell. Autoimmunity and the Gut. Autoimmune Dis. 2014.

Escames G, et al. Mitochondrial DNA and Inflammatory Diseases. Hum Genet. 2012 Feb; 131(2): 161-73.

Stojanovich L and Marisavljevich D. Stress as a Trigger of Autoimmune Disease. Autoimmune Rev. 2008 Jan; 7(3): 209-13.

A M Ercolini and S D Miller. The Role of Infections in Autoimmune Disease. Clin Exp Immunol. 2009 Jan; 155(1): 1-15.

Karyn Shanks MD. How to Heal Fatigue with Energy Nutrition. 2019.

Karyn Shanks MD. How to Optimize Energy with the FINE Food Plan. 2019.

Karyn Shanks MD. How to Optimize Protein for Energy and Vitality. 2019.

Sarah Ballantyne PhD. The Paleo Approach: Reverse Autoimmune Disease and Heal Your Body. 2013. Encyclopedia of the food-gut-autoimmune connection.

Karyn Shanks MD. How to Boost Energy with Ketosis and Intermittent Fasting. 2019.

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