The Importance of Digestion & Nutrition in Chronic Disease

The gastrointestinal 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.

Close to 100 million Americans suffer from some form of digestive problem.6 More than 40% of people worldwide have functional gastrointestinal disorders, with women reporting greater prevalence than men.7 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.

Kara Parker, MD, is a Functional Medicine clinician at the Whittier Clinic in Minnesota.

Nutritional Deficiencies

Gastrointestinal diseases are often associated with nutritional deficiencies.8 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.9

Deficiencies in zinc and vitamins A and D may reduce natural killer cell function, whereas supplemental zinc or vitamin C may enhance their activity.9 Vitamin D has been shown to play a role in intestinal defense by suppressing microbial invasion into the epithelium. Vitamin D deficiency has been identified in 82% of irritable bowel disease patients, and has been linked generally to defective epithelial processes. Therapy targeting vitamin D3 signaling has been suggested for treatment of inflammatory diseases, affecting both innate and adaptive immune functions.10 Targeted nutrition that considers individual genetic make-up, epigenetics, and microbiota composition may represent a platform for successful prevention and disease control.9

For example, liver, pancreatic, and inflammatory bowel diseases are often associated with nutritional difficulties and may necessitate nutritional therapy.8 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.8

Antioxidants like vitamin C or polyphenols (e.g., curcumin, quercetin, green tea polyphenols) may have beneficial effects to improve non-alcoholic fatty liver disease (NAFLD).8 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.8 A 2019 case-controlled study indicates a possible protective association between functional foods and the adoption of the Mediterranean diet and gastrointestinal diseases.11

Patients with inflammatory bowel disease (IBD) may experience micronutrient deficiencies due to losses from diarrhea and/or inadequate dietary intake.8,12 The most common micronutrient deficiencies are iron, calcium, selenium, zinc, and magnesium depletion. Vitamin deficiencies include all vitamins, but in particular B11, 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 pre-clinical studies, mainly in mouse models, where the active form of vitamin D has been shown to regulate gastrointestinal microbiota function and promote an anti-inflammatory response.8,12

Clearly, 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 work up and treat patients who present with conditions, signs, and symptoms indicative of gastrointestinal dysfunction. For more information on topics related to digestion and chronic disease, please visit the following links:

Learn More About gut Dysfunction and Chronic Conditions

Macronutrient Malnutrition: Not Limited to Developing Nations

Heal the Gut With the IFM Elimination Diet

Managing SIBO Through Dietary Interventions


  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 August 1, 2019.
  7. Sperber AD, Bangdiwala Sl, Drossman DA, et al. Worldwide prevalence and burden of functional gastrointestinal disorders, results of Rome Foundation Global Study. Gastroenterology. Published online April 12, 2020. doi:10.1053/j.gastro.2020.04.014
  8. 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
  9. 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
  10. Yin K, Agrawal DK. Vitamin D and inflammatory diseases. J Inflamm Res. 2014;7:69-87. doi:10.2147/JIR.S63898
  11. 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
  12. W?drychowicz A, Zaj?c 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

Related Insights