A Functional Nutrition Approach to Autoimmunity

November 15th, 2022

More than 24 million Americans suffer from various autoimmune disorders and the numbers continue to rise (1). Unfortunately, these patients often struggle with symptoms for years and see, on average, six different providers before getting a diagnosis (2). As a nutrition professional, you’ve probably encountered patients with these types of conditions and wondered how you can help.  In this article we’ll describe how autoimmune diseases develop and showcase how you can use the IFN Academy STAIN © model to target the root causes of and reverse negative autoimmune symptoms.

What is Autoimmune Disease?

Autoimmune disease results when your immune system gets confused about what’s friend and what’s foe. Instead of attacking potentially problematic bacteria, viruses, and parasites, your body begins to assault its own tissues and organs as if they’re invaders. As a result, patients with autoimmune diseases can experience a variety of symptoms like (2):

  • Fatigue
  • Swollen glands
  • Unexplained weight changes
  • Muscle weakness
  • Skin issues
  • Unexplained fevers
  • Digestive distress
  • Joint pain and/or swelling
  • Brain fog

In order to help patients heal, you have to understand how autoimmune diseases develop in the first place. While there’s a strong genetic link, only about 10 percent of people with a genetic predisposition go on to develop an autoimmune disease (2).  In fact, the development of autoimmunity requires the perfect storm of genetics, environmental triggers, and increased intestinal permeability (leaky gut) (3).  Let’s take a closer look at how the loss of gut barrier function can trigger the autoimmune cascade.

The Gut-Autoimmune Disease Connection

The small intestinal lining is prone to damage, which can spell trouble for people who are predisposed to autoimmune conditions. To understand why, you need a little background on how the gut barrier is regulated.

The epithelial cells of the small intestine are connected by a series of tight junctions and desmosomes, which are active and modifiable. The zonulin family of proteins regulate these tight junctions and when zonulin is up-regulated the loss of gut barrier function can result (3).  Bacterial toxins and large undigested food particles can then cross over into the systemic circulation, which triggers the immune system and the upregulation of pro-inflammatory cytokines (3). If this process continues unchecked, clinical disease can develop, assuming the other factors are present (environmental trigger and genetics) (3).

Source: https://pubmed.ncbi.nlm.nih.gov/33371435/

While the release of zonulin can be prompted by many factors, two of the most powerful are bacterial exposure (i.e. poor gut microbiome balance) and gliadin (the protein found in wheat) (4). Since poor gut health is a universal feature in autoimmunity, the gut is the perfect place for functional nutritionists to start when working with any person with an autoimmune disease (5).

Let’s take a look at an autoimmune case study and how to use the STAIN © model to target root causes.


Source: Integrative and Functional Nutrition Academy™, LLC. © 2022. All Rights Reserved.


Case Study: Aplastic anemia-paroxysmal nocturnal hemoglobinuria syndrome (AA-PNH)

Aplastic anemia (AA) is a rare immune-mediated blood disorder where new red blood cell formation is altered (6).   Patients can experience:

  • Significant fatigue
  • Shortness of breath with exertion
  • Frequent infections
  • Irregular heart rate
  • Death

Some people with AA can also develop paroxysmal hemoglobinuria syndrome (PNH), a disorder of the bone marrow where red blood cells are broken down more rapidly than normal (7). AA can lead to PNH and vice versa. AA-PNH syndrome is rare and thought to be caused by radiation and chemo therapy, drug or toxin exposure, autoimmune or rheumatologic diseases, infections, and/or nutritional deficiencies.

Conventional treatment can include bone marrow transplant, but in patients with AA-PNH syndrome caused by an autoimmune process the preferred treatment is immunosuppressive therapy (6).  Immunosuppressive drugs help to squelch the immune cells that are damaging the bone marrow, which allows new blood cells to be created.

While conventional treatment with medications is necessary in a case like this, functional nutritionists still have an important role to play when it comes to targeting the underlying cause(s) of autoimmune disease symptoms. The end result of nutrition therapy will be improved quality of life and also disease parameters.

Tiffany, a 34-year-old pharmacist, was diagnosed with AA-PNH syndrome after struggling with fatigue for several months. She began conventional treatment with an immunosuppressant early after her diagnosis but her labs and symptoms continued to worsen. Another medication was added a few months later but she didn’t experience any significant improvements. Tiffany decided to try nutrition therapy to improve her fatigue, cell counts, and to address her gastrointestinal symptoms.

Tiffany has a history of acne, Epstein-Barr virus, yeast overgrowth, and urinary tract infections. She works in a medical hospital and is on-call for her local hospice. Tiffany wasn’t sleeping well and had high stress related to her career. She shared that her diagnosis had taken a toll on her mental health and her fatigue made it difficult to exercise or focus on eating well. She was taking her prescription medications but also took magnesium oxide, a multivitamin, folic acid, and vitamin C. Her initial symptom score was 88 indicating severe symptoms.

Initial care plan:

  • Meditation and/or yoga for 10 to 20 minutes twice per day to target the unmanaged Stress and mental health.
  • Sleep hygiene techniques with the goal of restful, restorative sleep.
  • Elimination diet excluding gluten, dairy, red meat, inflammatory oils and additives, eggs, peanuts, corn, soy, caffeine, pork, and chocolate for eight weeks to begin to target gut health, Nutritional factors, Adverse food reactions, and Toxins.
  • L-glutamine powder (5 grams per day) for eight weeks to target assumed intestinal permeability.
  • Turmeric (450 milligrams three times per day) to help reduce inflammation and target gut health.
  • Lactobacillus/bifidobacterium probiotic for gut health.
  • Multivitamin to fill Nutrient gaps.
  • GI-Map stool testing to assess gut microbiome health and Infection.
  • Exercise as able to target deToxification, gut health, and energy level.

After five weeks, Tiffany’s symptom score had dropped to 30 and she said she had much more energy and less brain fog. She was sleeping better, had more focus, and her stress was better controlled. Tiffany was exercising despite low energy and felt exercise was helpful overall. Her AA-PNH syndrome labs had also improved:

  • Platelets increased from 29,000 to 58,000
  • Hemoglobin increased from 8.5 to 9.7g/dL
  • Absolute neutrophil count increased from 550 to 1140

Tiffany had a vitamin D level of 30 (suboptimal for those with autoimmunity) and her GI-Map stool testing indicated she was not digesting her food well and had some microbiome features common in autoimmunity.

Follow-up care plan:

  • Vitamin D3/K2 (5,000 units per day) with a goal vitamin D level of 50 to 80 ng/mL.
  • Change her folic acid supplement to methylfolate.
  • Continue vitamin C 1,000 milligrams to target immune system function.
  • Vitamin B 500 milligrams, vitamin B6 100 milligrams, and vitamin E 800 units per day for eight weeks to target gut health and stress.
  • Pancreatic enzymes prior to each meal ongoing to improve digestion and nutrient absorption.
  • Fatty fish three times per week ongoing for inflammation, gut health, and mental health.
  • Avoid personal care and home cleaning products with toxic chemicals.
  • Reintroduce high quality eliminated foods systematically after 8 weeks of the elimination diet.

After six months, Tiffany’s symptom score was down to 14, she was having solid bowel movements for the first time in years, and she had resumed a regular exercise program. Tiffany added pork, red meat, peanuts, and non-GMO corn back to her meal plan and she was continuing to avoid sugar and caffeine.  Her AA-PNH labs also continued to improve:

  • Platelets increased to 61,000
  • Hemoglobin increased to 10.4g/dL
  • Absolute neutrophil count increased to 1530
  • White blood cells increased from 2.0 to 3.34

Tiffany describes herself as a recovering busy-bee.  She’s taken up yoga to manage her stress and anxiety and has become a certified yoga instructor.

The Bottom Line

Autoimmune diseases can be difficult to manage and conventional treatments may not always be effective. Functional nutritionists have an opportunity to positively impact the quality of life and disease outcomes in patients with autoimmunity by using a root-cause approach that targets stress, toxins, adverse food reactions, infections, and nutritional imbalances.

Sign up for your IFN Academy training TODAY to learn how to use a whole-body systems approach and root-cause analysis to help your patients heal and thrive!

Kellie Blake RDN, LD, IFNCP



  1. National Institute of Environmental Health Sciences. “Autoimmune Disease” Retrieved from: https://www.niehs.nih.gov/health/topics/conditions/autoimmune/index.cfm Accessed September 29, 2022
  2. Vojdani, A. (2019). Food-Associated Autoimmunities: When Food Breaks Your Immune System (1st ed). A&G Press
  3. Fasano, A (2012) Zonulin, regulation of tight junctions, and autoimmune diseases. Annals of the New York Academy of Sciences. Jul 1258 (1): 25-33; DOI: 10.1111/j.1749-6632.2012.06538.x
  4. Fasano A. Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer. Physiol Rev. 2011;91(1):151-175. doi:10.1152/physrev.00003.2008
  5. Paray BA, Albeshr MF, Jan AT, Rather IA. Leaky Gut and Autoimmunity: An Intricate Balance in Individuals Health and the Diseased State. Int J Mol Sci. 2020;21(24):9770. Published 2020 Dec 21. doi:10.3390/ijms21249770
  6. Peslak, S., Olson, T., and Babushok, D. (2017) Diagnosis and Treatment of Aplastic Anemia. Current Treatment Options in Oncology.  Nov 16; 18(12): 70; doi: 10.1007/s11864-017-0511-z
  7. Brodsky, R. (2014) Paroxysmal nocturnal hemoglobinuria. Blood.  Oct 30; 124(18): 2804-2811; DOI: 10.1182/blood-2014-02-522128