The Importance of Digestion & Nutrition in Chronic Disease

Cute little girl helping her dad making healthy salad
Read Time: 4 Minutes

The gastrointestinal (GI) tract plays a central role in many chronic, systemic diseases. In functional medicine, the GI tract is often an important starting point in improving overall health. A complex, living system, the intestine protects the body from external influences based on three constituents that are in permanent dialogue with one another: the microbiota, mucosal barrier, and immune system.1 Dysfunction in this system can wreak havoc throughout the body and has been linked to allergies,2 arthritis,3 autoimmune disease,4 chronic fatigue,5 and more.

Millions of Americans suffer from some form of digestive problem,6,7 and more than 40% of people worldwide have functional gastrointestinal disorders, with women reporting greater prevalence than men.8 How can practitioners incorporate new research on barrier integrity, digestion, absorption, gut flora, and nutritional insufficiencies into the diagnosis and management of patients with digestive dysfunction and chronic diseases?

In the following video, IFM educator Kara Parker, MD, talks about the physiology of digestion and how it can be optimized to improve overall health.

(Video Time: 2 minutes) Kara Parker, MD, IFMCP, is a board-certified family doctor who has been practicing functional, integrative, and lifestyle medicine at Hennepin Healthcare with a low resource population for almost 20 years. She is the medical director of the Whittier Clinic Group Visits program and has presented nationally on how to create lifestyle and functional medicine shared medical appointments.

Nutritional Deficiencies and Immunity

Gastrointestinal diseases are often associated with nutritional deficiencies.9 Immunonutrition—the potential to modulate the activity of the immune system by interventions with specific nutrients—has also emerged as a clinically important concept, highlighting the importance of nutrients such as vitamins A, C, E, and D, folic acid, beta carotene, and trace elements such as zinc, selenium, manganese, and iron to the gut microbiome.10

  • Deficiencies in zinc and vitamins A and D may reduce natural killer cell function, whereas supplemental zinc or vitamin C may enhance their activity.10
  • Vitamin D has been shown to play a role in the control of gut epithelial permeability,11 and studies suggest that oral vitamin D supplementation may be a beneficial adjunctive treatment for chronic inflammatory diseases such as inflammatory bowel disease (IBD).12

Liver, pancreatic, and inflammatory bowel diseases are often associated with nutritional difficulties and may necessitate nutritional therapy.9 A study in the Journal of Clinical Medicine hints at the importance of screening these patients for protein depletion, trace elements deficiency, and malnutrition prior to initiating nutritional intervention.9

Antioxidants like vitamin C or polyphenols (e.g., curcumin, quercetin, or green tea polyphenols) may have beneficial effects to improve non-alcoholic fatty liver disease (NAFLD).9,13 Epidemiological studies and clinical trials suggest that the Mediterranean diet, which is characterized by a high content of antioxidants and fiber, a balanced lipid profile, and a low content of simple sugar, may be an effective diet for the management of NAFLD.9,14 A 2019 case-controlled study indicates a possible protective association between functional foods and the adoption of the Mediterranean diet and gastrointestinal diseases.15

Patients with IBD may experience micronutrient deficiencies due to losses from diarrhea and/or inadequate dietary intake.9,16 The most common micronutrient deficiencies are iron, calcium, selenium, zinc, and magnesium depletion. Vitamin deficiencies include all vitamins but in particular B12, folic acid, and vitamins A, D, and K. Studies suggest that vitamin D may play a role in the pathophysiology of IBD,17 and potential benefits of vitamin D in the therapeutic treatment of IBD are supported by randomized controlled trials and observational studies.18 A proposed mechanism suggests that the active form of vitamin D regulates gastrointestinal microbiota function and promotes an anti-inflammatory response.9,11 


Treating any nutritional deficiency is essential for gastrointestinal disease interventions. However, proper digestive functioning along the GI tract is needed for adequate nutrient absorption. For example, poor stomach acid secretion known as hypochlorhydria negatively impacts digestion of food and can lead to a variety of issues, most notably micronutrient deficiencies that exacerbate malnutrition and that may further impair immune function. Pancreatic insufficiency also impacts absorption of nutrients and may lead to vitamin and mineral deficiencies. Fat malabsorption, one of the most common malabsorption syndromes,19 is another example. In this case, nutrient signaling dysfunction and digestive enzyme insufficiency in the small intestine impairs lipid digestion, can cause steatorrhea, and may lead to deficiencies of fat-soluble vitamins.


The relationship between gastrointestinal dysfunction, nutrition, and chronic disease is multifaceted, compelling, and complex. The functional medicine model provides practitioners with the foundational background, insight, and in-depth clinical thinking to confidently assess and treat patients who present with conditions, signs, and symptoms indicative of gastrointestinal dysfunction.

IFM members also have access to the expansive IFM Toolkit, which has valuable clinical assessment tools and patient handouts specific to healthy digestion. The Testing for Low Stomach Acidity handout is a tool that describes the importance of adequate levels of stomach acid and the symptoms and potential treatment for hypochlorhydria. The Mindful and Intuitive Eating patient handout explores the benefits of mindful eating practices, including optimal digestion, and provides patients helpful tips for implementation and sustainability.

Learn more about the relationship between digestion and chronic disease at IFM’s GI Advanced Practice Module (APM).

Learn More About gut Dysfunction and Chronic Conditions

Related Articles

The Hidden Hunger: Micronutrient Deficiencies

Heal the Gut With the IFM Elimination Diet

Managing SIBO Through Dietary Interventions

Identifying the Root Causes of IBS


  1. Alemao CA, Budden KF, Gomez HM, et al. Impact of diet and the bacterial microbiome on the mucous barrier and immune disorders. Allergy. 2021;76(3):714-734. doi:10.1111/all.14548
  2. Akagawa S, Kaneko K. Gut microbiota and allergic diseases in children. Allergol Int. 2022;71(3):301-309. doi:10.1016/j.alit.2022.02.004
  3. Liu S, Li G, Xu H, et al. “Cross-talk” between gut microbiome dysbiosis and osteoarthritis progression: a systematic review. Front Immunol. 2023;14:1150572. doi:10.3389/fimmu.2023.1150572
  4. Christovich A, Luo XM. Gut microbiota, leaky gut, and autoimmune diseases. Front Immunol. 2022;13:946248. doi:10.3389/fimmu.2022.946248
  5. König RS, Albrich WC, Kahlert CR, et al. The gut microbiome in myalgic encephalomyelitis (ME)/chronic fatigue syndrome (CFS) [published correction appears in Front Immunol. 2022;13:878196]. Front Immunol. 2022;12:628741. doi:3389/fimmu.2021.628741
  6. Almario CV, Ballal ML, Chey WD, Nordstrom C, Khanna D, Spiegel BMR. Burden of gastrointestinal symptoms in the United States: results of a nationally representative survey of over 71,000 Americans. Am J Gastroenterol. 2018;113(11):1701-1710. doi:1038/s41395-018-0256-8
  7. Mathews SC, Izmailyan S, Brito FA, Yamal JM, Mikhail O, Revere FL. Prevalence and financial burden of digestive diseases in a commercially insured population. Clin Gastroenterol Hepatol. 2022;20(7):1480-1487.e7. doi:1016/j.cgh.2021.06.047
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  11.  Vernia F, Valvano M, Longo S, Cesaro N, Viscido A, Latella G. Vitamin D in inflammatory bowel diseases. Mechanisms of action and therapeutic implications. Nutrients. 2022;14(2):269. doi:10.3390/nu14020269
  12.  Guo Y, Zhang T, Wang Y, Liu R, Chang M, Wang X. Effects of oral vitamin D supplementation on inflammatory bowel disease: a systematic review and meta-analysis. Food Funct. 2021;12(17):7588-7606. doi:10.1039/d1fo00613d
  13.  Yang K, Chen J, Zhang T, et al. Efficacy and safety of dietary polyphenol supplementation in the treatment of non-alcoholic fatty liver disease: a systematic review and meta-analysis. Front Immunol. 2022;13:949746. doi:3389/fimmu.2022.949746
  14.  Haigh L, Kirk C, El Gendy K, et al. The effectiveness and acceptability of Mediterranean diet and calorie restriction in non-alcoholic fatty liver disease (NAFLD): a systematic review and meta-analysis. Clin Nutr. 2022;41(9):1913-1931. doi:1016/j.clnu.2022.06.037
  15.  Elmaliklis I-N, Liveri A, Ntelis B, Paraskeva K, Goulis I, Koutelidakis AE. Increased functional foods’ consumption and Mediterranean diet adherence may have a protective effect in the appearance of gastrointestinal diseases: a case-control study. Medicines. 2019;6(2):50. doi:10.3390/medicines6020050
  16.  Zupo R, Sila A, Castellana F, et al. Prevalence of zinc deficiency in inflammatory bowel disease: a systematic review and meta-analysis. Nutrients. 2022;14(19):4052. doi:3390/nu14194052
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  19.  Zuvarox T, Belletieri C. Malabsorption syndromes. StatPearls Publishing. Updated July 25, 2022. Accessed June 28, 2023.

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