Heal the Microbiome With the IFM Elimination Diet

Approximately 4% of American adults have a food allergy, according to a 2017 study.1 Researchers reviewed nearly three million medical records identifying more than 97,000 patients who suffered from one or more food allergies or an intolerance to food.1 More than 170 foods have been reported to cause reactions in the US, with eight major food allergens—milk, eggs, peanuts, tree nuts, wheat, soy, fish, and crustacean shellfish—responsible for most of the serious food allergy reactions.2 In the pediatric population, approximately 5% of children experience an anaphylactic food allergy.3

The gold standard for identifying food allergies is the elimination diet.4,5 IFM’s Elimination Diet is designed to clear the body of foods and chemicals that the patient may be sensitive or allergic to, improve the body’s ability to handle and dispose of those substances, support the microbiome, reduce inflammation, and increase phytonutrients.

The Elimination Diet is a short-term, three-week program that requires the patient to remove certain foods and food categories from their diet. With careful reintroduction, the IFM Elimination Diet helps patients identify the foods that may trigger their symptoms. For patients with anaphylactic, IgE-mediated food allergies, reintroduction should only occur in the presence of trained healthcare professionals.

After completion of the three-week IFM Elimination Diet, patients undergo a food reintroduction process. The goal is to expand the variety of healthy foods available to an individual for daily intake. Reintroduction involves adding back one food at a time and observing whether that food is associated with negative symptoms.

In the following video, IFM educator Elizabeth Boham, MD, MS, RD, discusses the importance of a careful reintroduction of foods during the IFM Elimination Diet.

IFM educator Elizabeth Boham, MD, MS, RD, is board certified in family medicine and a registered dietitian with a strong background in Functional Medicine.

For food reactions including sensitivities and intolerances, reintroduction may often safely occur at home, after the Elimination Diet has reduced inflammation and stress on the body. Mechanistic studies suggest that dietary components can modulate key pathways to inflammation, including sympathetic activity, oxidative stress, transcription factor nuclear factor-kappa B (NF-?B) activation, and proinflammatory cytokine production.6 “Westernized diets” that promote inflammation are high in refined starches, sugar, and saturated and trans-fats and low in omega-3 fatty acids and natural antioxidants and fiber from fruits, vegetables, and whole grains.6 Higher fruit and vegetable intake, however, has been associated with lower oxidative stress and inflammation.6,7

Following reintroduction, foods that continue to provoke symptoms (physical, mental, and emotional) are avoided for an additional three to six months, at which time reintroduction is attempted again. Once the gut is healed, many foods that initially caused sensitivities may be reintroduced into a meal plan without symptoms. Healing the gut and being able to successfully reintroduce foods is important, as eating the same few foods day after day does not provide the body with the full array of phytonutrients necessary for overall health. A diet with a large diversity of foods helps ensure that the body gets essential nutrients and is especially important for those who have digestive issues.

Research on the Elimination Diet for food sensitivities is still emerging and quite promising. For instance, in a 2013 study evaluating the therapeutic potential of the immunoglobulin G (IgG)-based elimination diet among migraine patients with irritable bowel syndrome (IBS), researchers found that the diet may effectively reduce symptoms from both disorders with possible positive impact on the quality of life of the patients.8

A 2015 study in children with eosinophilic esophagitis (EoE) suggested that an allergy-driven elimination diet is an efficient complementary treatment to corticosteroids.9 All children with EoE and mild symptoms had resolution of symptoms and normal eosinophils in the esophageal mucosa a year after an allergy-driven elimination diet.9

A 2018 case study in a 22-year-old patient with eosinophilic gastroenteritis treated with oral prednisolone showed that symptoms improved with the initial treatment but recurred when the prednisolone was tapered to a low dose.10 Following a multiple food elimination diet, including milk, soy, eggs, wheat, nuts, seafood, and rice, and then reintroduction of these foods, it was discovered that dairy products and eggs were the causative foods for her symptoms. The patient continued the elimination diet as an outpatient and was no longer affected by severe abdominal distress. At the time of the case writing, she was in good condition and without prednisolone administration.10

Emerging research continues to show that symptoms and conditions that have failed to respond to the standard of care may resolve when a patient follows an elimination diet. After the initial period of eliminating foods, many chronic symptoms should improve or disappear. When the burden on the immune system is decreased, the body has an opportunity to heal. During the elimination period, it is important to make sure that the diet is still enjoyable and nutrient-dense. The road to optimum health starts with decreasing the burden on the immune system while ensuring adequate nutrition.

That said, it is important to emphasize that elimination diets are designed to be short-term. Long-term dietary restrictions have been associated with nutrient deficiencies.11 In a study of patients with ulcerative colitis and Crohn’s disease, the rate of malnutrition in patients was high, with high rates of deficiency in iron, calcium, vitamin B12, and vitamin D.11 One of the causes for malnutrition was a dietary adjustment based on the patient’s own experience or belief.11 The goal of the IFM Elimination Diet is to heal the system and then return the patient to a wide and varied diet that provides adequate nutrition.

The IFM Elimination Diet has been found to be generally well tolerated, and most individuals have reported increased energy, mental alertness, a decrease in muscle or joint pain, and a general sense of improved well-being. IFM’s Elimination Diet is available to all members in the IFM Toolkit, along with a wealth of other resources, including the Food Reintroduction Symptom Tracker. This important guide helps practitioners and patients to reintroduce only one new food at a time and assess the body’s response to that food by keeping track of symptoms.

Learn more about inflammation, immune responses to food, and more at IFM’s GI Advanced Practice Module


  1. Acker WW, Plasek JM, Blumenthal KG, et al. Prevalence of food allergies and intolerances documented in electronic health records. J Allergy Clin Immunol. 2017;140(6):1587-1591. doi:10.1016/j.jaci.2017.04.006.
  2. NIAID-Sponsored Expert Panel. Guidelines for the diagnosis and management of food allergy in the United States: report of the NIAID-sponsored expert panel. J Allergy Clin Immunol. 2010;126(6 Suppl):S1-S58. doi:10.1016/j.jaci.2010.10.007.
  3. Jackson KD, Howie LD, Akinbami LJ. Trends in allergic conditions among children: United States, 1997-2011. NCHS Data Brief. 2013;(121):1-8.
  4. Wood RA. Diagnostic elimination diets and oral food provocation. Chem Immunol Allergy. 2015;101:87-95. doi:10.1159/000371680.
  5. Werfel T, Erdmann S, Fuchs T, et al. Approach to suspected food allergy in atopic dermatitis. Guideline of the Task Force on Food Allergy of the German Society of Allergology and Clinical Immunology (DGAKI) and the Medical Association of German Allergologists (ADA) and the German Society of Pediatric Allergology (GPA). J Dtsch Dermatol Ges. 2009;7(3):265-271. doi:10.1111/j.1610-0387.2008.06901.x
  6. Kiecolt-Glaser JK. Stress, food, and inflammation: psychoneuroimmunology and nutrition at the cutting edge. Psychosom Med. 2010;72(4):365-369. doi:10.1097/PSY.0b013e3181dbf489.
  7. Calder PC, Albers R, Antoine JM, et al. Inflammatory disease processes and interactions with nutrition. Br J Nutr. 2009;101(Suppl 1):S1-S45. doi:10.1017/S0007114509377867.
  8. Aydinlar EI, Dikmen PY, Tiffikci A, et al. IgG-based elimination diet in migraine plus irritable bowel syndrome. Headache. 2013;53(3):514-525. doi:10.1111/j.1526-4610.2012.02296.x.
  9. Syrigou E, Angleakopoulou A, Zande M, Panagiotou I, Roma E, Pitsios C. Allergy-test-driven elimination diet is useful in children with eosinophilic esophagitis, regardless of the severity of symptoms. Pediatr Allergy Immunol. 2015;26(4):323-329. doi:10.1111/pai.12389.
  10. Okimoto E, Ishimura N, Okada M. Successful food-elimination diet in an adult with eosinophilic gastroenteritis. ACG Case Rep J. 2018;5:e38. doi:10.14309/crj.2018.38.
  11. Lim HS, Kim SK, Hong SJ. Food elimination diet and nutritional deficiency in patients with inflammatory bowel disease. Clin Nutr Res. 2018;7(1):48-55. doi:10.7762/cnr.2018.7.1.48.

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