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Functional Medicine Treatment for Malabsorption Syndrome

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Functional Medicine Treatment for Malabsorption Syndrome

The gastrointestinal tract has a primary role in absorbing fats, proteins, carbohydrates, and micronutrients. When the processes necessary for digestion and absorption fail, food particles are not properly assimilated, and malabsorption can occur. The key area involved in absorption is the small intestines.

A healthy functioning digestive tract is critical for the absorption of nutrients. This article will discuss malabsorption syndrome and a functional medicine approach to testing and treatment.  


What is Malabsorption Syndrome?

An optimally functioning digestive tract will take the foods you eat, break them down, and then absorb the nutrients. Malabsorption Syndrome is when your small intestine is not absorbing nutrients properly due to various failed digestive system processes. Digestion consists of three steps: breaking down the food, assimilating the nutrients from the food, and eliminating waste. The second step is where malabsorption occurs. You might be able to break down foods into their nutritional components. But, if your body cannot properly take in the macronutrients and micronutrients, it leads to malabsorption and malnutrition.

What Are The Different Types Of Malabsorption Disorders?

Carbohydrate Malabsorption

A disruption in sugar digestion can lead to carbohydrate malabsorption. When foods high in carbohydrates, like grains, are not broken down and absorbed through the small intestines, it leads to digestive complications. Unabsorbed sugars will become the feeding ground for bacteria residing in your colon. As these bacteria feed on the sugar, fermentation occurs, which produces gases like hydrogen and methane. Another by-product of fermentation is short-chain fatty acids which pass through the gastrointestinal tract and causes fatty stools. Conditions that contribute to carbohydrate malabsorption are:

  • Enzyme deficiency
  • Mucosal injury
  • Celiac Disease
  • Tropical Sprue
  • Intestinal Lymphangiectasia
  • IBD

Fat Malabsorption

Defects leading to an inability to digest and absorb fats are one of the most common forms of malabsorption. Processing lipids for absorption occurs via emulsification. The combination of chewing and enzyme release in the mouth begins the process. As food moves down the digestive tract, the stomach and pancreas release lipolytic enzymes. Bile salts then add to the process by increasing pH, which helps transform the lipid particles into micelles. The absorption of fat particles in the form of micelles happens in the jejunum (proximal small intestines). Disruption can occur during the process of transferring fat to micelles, leading to the body's inability to absorb this macronutrient. Conditions that can lead to this are:

  • Decreased pH in the small intestines
  • Crohn's disease
  • Celiac disease
  • Resection surgeries like bariatric surgery
  • SIBO
  • Bile acid insufficiency
  • Ulcerative colitis (UC)
  • Liver disease
  • Cholestasis
  • Pancreatic insufficiency conditions
  • Cystic Fibrosis
  • Gallbladder diseases
  • Whipple disease

Protein Malabsorption

Protein malabsorption occurs when the small intestine cannot break down or transport certain amino acids across its brush border. Someone with this condition more than likely has a food protein intolerance such as gluten, casein, or other milk proteins. Other conditions that put someone at risk for protein malabsorption are:

Bile Acid Malabsorption

When there is a lack of bile secreted from the liver and gallbladder, it can lead to bile salts triggering water secretion. This leads to chronic diarrhea as a result of bile acid malabsorption.

Conditions associated with this type of malabsorption are:

What are The Symptoms of Malabsorption Syndrome?

Initial Symptoms:

  • Indigestion
  • Abdominal pain
  • Abdominal distension
  • Bloating
  • Gas
  • Diarrhea
  • Steatorrhea

Untreated malabsorption syndrome can lead to symptoms of malnutrition due to micronutrient depletion, which includes, but is not limited to:

  • Dry skin and lesions
  • Frequent infections
  • Muscle wasting
  • Unintentional weight loss
  • Dehydration
  • Edema
  • Bleeding gums and nosebleeds
  • Night blindness
  • Amenorrhea
  • Growth delays
  • Irritability
  • fatigue
  • Anemia
  • Dizziness

What Causes Malabsorption Syndrome?

Food Intolerances

Gastrointestinal disease processes can increase malabsorption when exposed to macronutrients or food components your body cannot tolerate. These foods are called food intolerances. For example, individuals with Celiac disease cannot tolerate gluten protein. Eating this will cause inflammation, an immune response, and malabsorption. Other common intolerances include foods in which someone lacks the necessary enzymes to break them down.

A good example would be fructose and lactose intolerance. Honey and dairy, foods high in fructose and lactose, can cause malabsorption if you lack the necessary enzymes. Some individuals may have food intolerances that are non-immunological and non-enzymatic but cause gastrointestinal distress due to other food composition or underlying disease processes.

Small Intestinal Damage

Inflammation and injury to the mucus membranes of the small intestines can prohibit the absorption of nutrients. The mucous lining of your intestines releases enzymes to break down food while simultaneously being the medium for nutrient absorption from the food. Inflammatory conditions like Ulcerative Colitis (UC) and Chron's, as well as autoimmune Celiac disease, can damage the intestinal lining, causing malabsorption. Other conditions impairing the small intestines include Whipple's disease, short bowel syndrome, SIBO, Zollinger-Ellison syndrome, radiation therapy, chemotherapy, and the overuse of certain medications.

Organ Dysfunction

Pancreatic, liver, and gallbladder conditions can all lead to malabsorption. In order to break down food, your body needs to produce and release digestive enzymes from your pancreas. Those enzymes act in conjunction with bile that is stored and released from your liver and gallbladder. Conditions like gallbladder disease, liver disease, cystic fibrosis, and pancreatic insufficiency can all stop these organs from functioning. Ultimately this will inhibit the breakdown of macronutrients and the small intestines' ability to absorb them.

Lymphatic Conditions

Your lymphatic system helps move nutrients into your bloodstream. If there is stagnant lymphatic flow, your body may not be capable of absorbing fats. Two specific conditions also impact lymphatic function- lymphangiectasia and lymphoma. Complications within the lymphatic system can also result in protein malabsorption, which can lead to symptoms of edema and ascites.

Functional Medicine Labs to Test for Root Cause of Malabsorption Syndrome


Obtaining a complete blood count (with differentials) test will help assess for anemias and infections that may result from malabsorption.

Comprehensive Metabolic Panel

Malabsorption syndrome can disrupt the body's electrolyte balance, have hepatic and renal involvement, or cause protein depletion. Getting a CMP can reveal if your minerals are imbalanced, whether or not these organ systems are in distress, and if your protein status is adequate.

SIBO Breath Test

Genova Diagnostics offers a 3-hour breath test that analyzes methane and hydrogen gas levels after ingesting a lactulose solution. Levels of these gases can determine if Small Intestinal Bacterial Overgrowth is contributing to your malabsorption. Common conditions that often benefit from results and course of treatment are Crohn's or Celiac disease.

Reactive Food Testing

Working with a functional medicine provider can help determine appropriate testing depending on whether a food intolerance, food sensitivity, or food allergy is suspected. Currently, there are a few enzymatic-related food intolerance breath tests that we can order. Commonwealth Diagnostics International offers Fructose, Lactose, or Sucrose Malabsorption Breath tests. While there is no mainstream comprehensive food intolerance test, there are food sensitivity and allergy tests. Alletess Laboratory offers a 184-item Food Sensitivity test that evaluates IgG immune-mediated reactions. Infinite Allergy offers a test measuring 88 common food antigens to test for IgE-mediated Food Allergies. Working closely with your healthcare provider can help determine which of these avenues provides you the most value.

Comprehensive Stool Analysis

Combining a comprehensive stool test with a food sensitivity panel can provide an overall picture of gut health. The GI-Map + Zonulin test by Diagnostic Solutions can detect a microbial imbalance and pick up microbes contributing to illness. This test can also objectively measure digestion, absorption, inflammation, and immune function. Zonulin, the marker for leaky gut, is a great indicator of intestinal permeability. High Zonulin indicates damage to the intestinal wall tight junctions, which can impact absorption.

Micronutrient Testing

Chronic malabsorption can lead to nutrient deficiencies. Utilizing a comprehensive test can help evaluate what nutrients you are deficient in. This is a great way to identify and target nutraceutical therapy while addressing the root cause of malabsorption.

Other Lab Test to Check

If all avenues have been investigated, and/or symptoms of Cystic Fibrosis are present, the next step would be a referral to a medical doctor that can evaluate you and run the proper test, such as a Sweat test.

Testing for Bile Acid Malabsorption involves a fecal bile acid test for stool acid levels or a Serum 7aC4 test. Both of these can be done by your primary care provider.

Endoscopy, with or without biopsy, is a valuable assessment tool to visualize the upper gastrointestinal tract. Anytime persistent pain, nausea, bloating, diarrhea, or indigestion occur, obtaining visualization can aid in proper diagnosis and treatment.

Gastrointestinal X-Ray is an additional first line of testing that can be done through your primary care provider to rule out any obstructive or inflammatory concerns of the gastrointestinal tract.

Functional Medicine Treatment for Malabsorption Syndrome


Depending on the cause of malabsorption, your dietary recommendations could vary. For someone who is lactose intolerant or has Celiac disease, avoiding the offending foods is recommended. If food sensitivities are the culprit, it is best to work with a holistic practitioner to do food sensitivity testing, implement an elimination diet, work on gut healing, and then slowly re-introduction. If an inflammatory-based condition like Crohn's or Ulcerative Colitis is the primary contributor, you could benefit from the Specific Carbohydrate Diet (SCD). One study of 400 IBD patients revealed that one-third of those that followed SCD went into symptomatic remission two months into this nutrition plan.

Supporting bile flow from the liver and gallbladder would be beneficial if you suffer from dysfunction in these organs. Functional foods like Artichokes and bitter foods like dandelion stimulate bile flow and protect the liver.

Herbs & Supplements

Althea Officinalis, also known as Marshmallow root, has therapeutic benefits in healing inflamed and damaged mucosal tissue. The antioxidant-rich mucilaginous component of this botanical is known to add a layer of protection over mucous membranes, which can help soothe the small intestines during the healing process.

Milk Thistle is a great botanical to utilize for its antioxidant and hepatoprotective properties. Incorporating this into a treatment plan for someone with liver disease can help decrease inflammation associated with the condition.

Taking exogenous digestive enzymes to help your GI tract break down macronutrients is a great way to assist absorption. Enzyme supplementation is especially important in cases of Pancreatic Insufficiency and Cystic Fibrosis.

Lifestyle Changes

Massage Therapy: Professional lymphatic drainage massage can be a wonderful tool to help move stagnant lymph. While there is limited evidence-based research on the topic, it is known that this type of massage is not recommended for those with Lymphoma, as you do not want to disrupt the affected lymph nodes.

Stress Management: A stress reduction practice can influence the gut-brain axis and relieve some symptoms. A review on the topic discusses how episodes of stress in conditions such as IBD can alter intestinal permeability and impede healing.

Exercise and Gut health: Research states that gut microbiome diversity has a positive correlation with aerobic exercise. Getting in a daily walk or a minimum of 150 minutes of weekly aerobic exercise is ideal. Other evidence suggests that Yoga can mitigate some of the symptoms associated with IBS, which may impact your malabsorption.


Malabsorption syndrome can be a result of one or multiple malabsorption conditions. Considering your symptoms, medical history, and how your symptoms have progressed are all essential factors in determining if a defect in your ability to absorb nutrients is occurring. Getting the basic testing done, such as a CBC, CMP, and X-ray, can help rule out some diagnoses. Further investigation into specialty labs and functional medicine testing can give more insight into the root cause. Considering your symptoms and labs, holistic medicine can relieve symptoms or be your path to healing.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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