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 microflora, 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 intestinal defense by suppressing microbial invasion into the epithelium. Therapy targeting vitamin D3 signaling has been suggested for treatment of inflammatory diseases, affecting both innate and adaptive immune functions.11

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 Epidemiological studies 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, is an appropriate diet for the management of NAFLD.9 A 2019 case-controlled study indicates a possible protective association between functional foods and the adoption of the Mediterranean diet and gastrointestinal diseases.12

Patients with inflammatory bowel disease (IBD) may experience micronutrient deficiencies due to losses from diarrhea and/or inadequate dietary intake.9,13 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. There are suggestions that in genetically predisposed individuals, vitamin D deficiency may be a contributing factor in the development of IBD. Beneficial effects of vitamin D in IBD are supported by randomized controlled trials and observational studies.14 A proposed mechanism suggests that the active form of vitamin D regulates gastrointestinal microbiota function and promotes an anti-inflammatory response.9,13 


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,15 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.

For more information on topics related to digestion and chronic disease, please visit the following links:

Learn More About gut Dysfunction and Chronic Conditions

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Managing SIBO Through Dietary Interventions

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  1. Bourlioux P, Koletzko B, Guarner F, Braesco V. The intestine and its microflora are partners for the protection of the host: report on the Danone Symposium “The Intelligent Intestine,” held in Paris, June 14, 2002. Am J Clin Nutr. 2003;78(4):675-683. doi:10.1093/ajcn/78.4.675
  2. Kyburz A, Müller A. The gastrointestinal tract microbiota and allergic diseases. Dig Dis. 2016;34(3):230-243. doi:10.1159/000443357
  3. Williamson L, Dockerty JL, Dalbeth N, Wordsworth BP. Gastrointestinal disease and psoriatic arthritis. J Rheumatol. 2004;31(7):1469-1470.
  4. Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol. 2012;42(1):71-78. doi:10.1007/s12016-011-8291-x
  5. Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE, Hanson MR. Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome. 2016;4(1):30. doi:10.1186/s40168-016-0171-4
  6. National Institute of Diabetes and Digestive and Kidney Diseases. Digestive diseases statistics for the United States. Published November 2014. Accessed July 13, 2022.
  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
  8. Sperber AD, Bangdiwala Sl, Drossman DA, et al. Worldwide prevalence and burden of functional gastrointestinal disorders, results of Rome Foundation Global Study. Gastroenterology. 2021;160(1):99-114.e.3. doi:10.1053/j.gastro.2020.04.014
  9. Storck LJ, Imoberdorf R, Ballmer PE. Nutrition in gastrointestinal disease: liver, pancreatic, and inflammatory bowel disease. J Clin Med. 2019;8(8):1098. doi:10.3390/jcm8081098
  10.  Aleksandrova K, Romero-Mosquera B, Hernandez V. Diet, gut microbiome and epigenetics: emerging links with inflammatory bowel diseases and prospects for management and prevention. Nutrients. 2017;9(9):962. doi:10.3390/nu9090962
  11.  Yin K, Agrawal DK. Vitamin D and inflammatory diseases. J Inflamm Res. 2014;7:69-87. doi:10.2147/JIR.S63898
  12.  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
  13.  Wedrychowicz A, Zajac A, Tomasik P. Advances in nutritional therapy in inflammatory bowel diseases: review. World J Gastroenterol. 2016;22(3):1045-1066. doi:10.3748/wjg.v22.i3.1045
  14.  Guzman-Prado Y, Samson O, Segal JP, Limdi JK, Hayee B. Vitamin D therapy in adults with inflammatory bowel disease: a systematic review and meta-analysis. Inflamm Bowel Dis. 2020;26(12):1819-1830. doi:1093/ibd/izaa087
  15.  Zuvarox T, Belletieri C. Malabsorption syndromes. StatPearls Publishing; 2021. Accessed July 13, 2022.

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