Improving Gut Health: Why does Malabsorption occur?

Functional medicine has a holistic mind-body approach to treating chronic conditions and addresses health issues by treating the root causes and not just the symptoms. One of the many therapeutic approaches in Functional Medicine is often to deeply analyze the gut. Since the gut is one of the most important organ systems within the body and supports a crucial micro-environment, ensuring a healthy gut often means limitless health benefits for both the mind and body.

The GI tract enables the absorption of Fats, carbohydrates, proteins, vitamins, minerals, and trace elements. However, impaired nutrient digestion or maldigestion is one of the most obvious signs of an unhealthy gut. Malabsorption occurs when the GI tract is unable to break down and absorb the nutrients efficiently, hence leading to the exacerbation of diseases and chronic health conditions.


Fat malabsorption:

Although the first step of lipid processing called emulsification begins in the mouth, only 15% of the total ingested fat gets digested before reaching the small intestine. The remaining 85% is processed directly in the Duodenum.

Factors that lead to Fat malabsorption:

– Decrease in Duodenal pH level below 6.5

– Loss in absorptive intestinal surface area and reduced exposure to digestive enzyme activity

– Small intestinal bacterial overgrowth and diffuse mucosal disease (such as Ulcerative Colitis)

– Insufficient bile activity and persistence of bile acids in the intestinal lumen

– Defective chylomicron/lipoprotein secretion and hidden lymphatic disorders can all be reasons behind Fat malabsorption.


Carbohydrate malabsorption:

Digestion and absorption of carbohydrates indicate the breakdown and absorption of starch, lactose, and sucrose in the diet. These polysaccharides need to be broken down into monosaccharides for appropriate absorption.

Carbohydrate digestion begins in the mouth with salivary amylase. The polysaccharides get further broken down by pancreatic amylase, and the remaining product gets further broken down and absorbed in the microvillus membrane of the small intestine.

Factors that lead to Carbohydrate malabsorption:

– Lack of activity or decreased enzyme synthesis for crucial enzymes such as Pancreatic Amylase, Lactase, Sucrase, and Trehalase. Inadequate disaccharidase activity leads to carbohydrate malabsorption.

– Functional loss of small intestinal mucosa (Entero-enteric fistula or Entero-colic fistula)

– Ingestion and deposition of unabsorbable carbohydrates such as Cellulose and Sorbitol.

– Bacterial overgrowth, blind loops, and autoimmune enteropathy.


Protein malabsorption: 

In an acidic environment, protein digestion and absorption start automatically in the stomach via proteolysis. Proenzymes become active at low pH and kick off the process, which depends on various other factors to be efficient and sustainable. For instance, Cholecystokinin (CCK), a hormone is responsible for pancreatic secretion and gallbladder contraction. It highly regulates gastric emptying, ingestion, digestion, and absorption of nutrients. However, the release of CCK depends on the release of amino acids in the stomach.

Factors that lead to protein malabsorption:

– Impaired pancreatic bicarbonate and protease secretion or activity.

– Lost absorptive intestinal surface area

– Diffuse Mucosal Injury

– Bowel resection


Vitamin, Mineral, and Trace Element malabsorption:

Several different intestinal transport mechanisms help with the absorption of minerals, vitamins, and trace elements.

Factors that lead to Vitamin, Mineral, and Trace Element malabsorption:

– Pathology associated with stomach and small intestine ( eg: Vit. B12 deficiency as a result of infection via helminths)

– Loss in absorptive intestinal surface area as a result of the long-term build-up of unwanted waste material within the intestine.

– Bacterial malabsorption and Fat malabsorption.

The silver lining, however, is that Functional Medicine and Functional Nutrition focus exclusively on gut health and can fix issues with nutrient malabsorption. As a result, many chronic illnesses can be healed or even managed more efficiently because the body gains its balance with the gut microbiome and natural absorption mechanisms.

If you or anyone you know have been battling chronic diseases or undergoing treatment for chronic gut-related problems, please contact The Functional Medicine Center for Personalized Care, LLC ( at 201-880-8247 or Specialized Therapy Associates at 201-488-6678 for our Integrative Mind-Body Health services. Our Integrative Mind-Body Health services incorporate Acupuncture, Functional Nutrition, IV Nutrition, Health Coaching, Exercise, Yoga, and Mind-Body Psychotherapy to support holistic healing and recovery.


Ishtiak Ahmed Chowdhury



Fernández-Bañares F, Monzón H, Forné M. A short review of malabsorption and anemia. World J Gastroenterol. 2009 Oct 7;15(37):4644-52. doi: 10.3748/wjg.15.4644. PMID: 19787827; PMCID: PMC2754512.

Goodman BE. Insights into digestion and absorption of major nutrients in humans. Adv Physiol Educ. 2010 Jun;34(2):44-53. doi: 10.1152/advan.00094.2009. PMID: 20522896.

Liddle RA. Cholecystokinin cells. Annu Rev Physiol. 1997;59:221-42. doi: 10.1146/annurev.physiol.59.1.221. Erratum in: Annu Rev Physiol 1998;60:XII. PMID: 9074762.

Misselwitz B, Butter M, Verbeke K, Fox MR. Update on lactose malabsorption and intolerance: pathogenesis, diagnosis and clinical management. Gut. 2019 Nov;68(11):2080-2091. doi: 10.1136/gutjnl-2019-318404. Epub 2019 Aug 19. PMID: 31427404; PMCID: PMC6839734.

Rinawi F, Iancu TC, Hartman C, Cohen H, Yarden-Bilavsky H, Lev MR, Shamir R. Fat malabsorption due to bile acid synthesis defect. Isr Med Assoc J. 2015 Mar;17(3):190-2. PMID: 25946774.

Shreiner AB, Kao JY, Young VB. The gut microbiome in health and in disease. Curr Opin Gastroenterol. 2015 Jan;31(1):69-75. doi: 10.1097/MOG.0000000000000139. PMID: 25394236; PMCID: PMC4290017.

Othman MO, Harb D, Barkin JA. Introduction and practical approach to exocrine pancreatic insufficiency for the practicing clinician. Int J Clin Pract. 2018 Feb;72(2):e13066. doi: 10.1111/ijcp.13066. Epub 2018 Feb 5. PMID: 29405509; PMCID: PMC5873407.

Owens SR, Greenson JK. The pathology of malabsorption: current concepts. Histopathology. 2007 Jan;50(1):64-82. doi: 10.1111/j.1365-2559.2006.02547.x. PMID: 17204022.








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