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A Functional Medicine Diarrhea Protocol: Comprehensive Lab Testing, Therapeutic Diet, and Supplements

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A Functional Medicine Diarrhea Protocol: Comprehensive Lab Testing, Therapeutic Diet, and Supplements

With an estimated 179 million cases annually, acute diarrhea is one of the most common illnesses in the United States. Worldwide, acute diarrhea is a leading cause of death in children under four. Chronic diarrhea, lasting longer than four weeks, affects approximately 5% of the population. Virtually all people will experience some type of diarrhea at some point in their lives. Keep reading to learn about the causes of diarrhea and functional medicine approaches to its treatment.


What Is Diarrhea?

Diarrhea is a gastrointestinal condition characterized by loose, watery bowel movements. In addition, loose stools may occur more frequently than usual. Diarrhea is classified by how long it lasts. Acute diarrhea lasts less than two weeks, persistent diarrhea lasts between two and four weeks, and chronic diarrhea persists longer than one month. Acute diarrhea is the second most commonly reported illness in the United States. Severe diarrhea can lead to dehydration, electrolyte imbalances, and shock, particularly in vulnerable populations. (19

Diarrhea Signs & Symptoms

The main symptom of diarrhea is passing loose, watery stools, often three or more times daily. However, depending on the cause, diarrhea may also be accompanied by at least one of the following symptoms (35): 

  • Fecal urgency
  • Blood and mucus in stool
  • Abdominal pain and cramping
  • Bloating
  • Gas 
  • Nausea and vomiting
  • Change in appetite
  • Fever and chills
  • Weight loss

What Causes Diarrhea?

The differential diagnosis for diarrhea is extensive. The chronicity of diarrhea will help to narrow the differential, as acute and persistent diarrhea have causes that differ from those of chronic diarrhea.

The leading causes of acute and persistent diarrhea are infections, traveler's diarrhea, and medication/supplement side effects. Viral, bacterial, and parasitic infections can cause diarrhea. Traveler's diarrhea is caused by consuming food or water contaminated by a pathogenic organism; it is most commonly acute, but some parasitic infections can go undetected, causing more chronic diarrhea. (35)

Many medications and supplements can cause diarrhea as a side effect. Antibiotics, antacids, laxatives, and chemotherapy drugs are examples of medicines that cause diarrhea (35). Magnesium, high doses of vitamin C, aloe vera, and fish oil are common supplements responsible for causing loose stool. 

Many gastrointestinal pathologies are responsible for causing loose stool, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS-D), celiac disease, fat malabsorption due to gallbladder or pancreatic disease, small intestinal bacterial overgrowth (SIBO), lactose intolerance and other adverse reactions to foods, and colon cancer.

Extraintestinal disorders can also cause diarrhea as a predominant symptom. Examples include hyperthyroidism, Addison's disease, endometriosis, and diabetes

Functional Medicine Labs to Test for Root Cause of Diarrhea

Many functional medicine tests can be ordered to assess the health and function of the gastrointestinal tract and determine the root cause of loose stool. Here are some of the most commonly ordered tests during a diagnostic evaluation of diarrhea. 

Blood Work

Routine blood work is standard in working up diarrhea, especially in chronic cases. 

A complete blood count (CBC) with differential can screen for signs of infection. Specific patterns in white blood cell distributions can differentiate between the chronicity and type of infection. Additionally, inflammatory bowel diseases may lead to gastrointestinal bleeding, leading to anemia, which can be diagnosed with this panel.

A comprehensive metabolic panel (CMP) assesses blood sugar, electrolytes, pH, and the liver, gallbladder, and kidney health. This thorough evaluation can indicate pathologies that cause and result from diarrheal diseases. 

Poorly managed or undiagnosed diabetes mellitus can cause nerve damage and intestinal dysmotility, leading to diarrhea (5). Hemoglobin A1c (HbA1c) is a three-month average of blood sugar most commonly used to diagnose diabetes. 

A hyperthyroid state increases the body's metabolic rate and can contribute to diarrhea through various mechanisms, which include increasing intestinal motility and altering fluid absorption in the intestines. Hyperthyroidism can be screened for with a thyroid panel, including TSH, free T4, and free T3.

While endoscopy is required for definitive diagnosis, a celiac panel is routinely ordered first as a less invasive and expensive means of ruling in the diagnosis of celiac disease. 

Comprehensive Stool Test

Comprehensive stool tests measure many gut-specific biomarkers helpful in assessing the health and function of overall gut function, integrity, and overall health. The biomarkers can be organized into broad categories that help assess digestive function, inflammation and immune function, infections, and intestinal dysbiosis. Comprehensive stool tests include conventional markers, such as pancreatic elastase, fecal fat, calprotectin, and stool cultures; however, they also go beyond these traditional markers to detect more subtle imbalances in intestinal permeability, digestion, and the microbiome, which standard tests cannot pick up. 

SIBO Breath Test

Hydrogen- and hydrogen sulfide-dominant subtypes of SIBO are strongly associated with diarrheal presentations. Food poisoning, a common cause of acute diarrhea, can induce immunological changes that generate small intestinal dysmotility, resulting in SIBO and persistent/chronic diarrhea even after the inciting infection has been treated. (8

The trio-smart breath test is the only SIBO test on the market capable of directly measuring all three gaseous byproducts (hydrogen, methane, and hydrogen sulfide) associated with the three types of SIBO. 

Adverse Food Reactions

Adverse food reactions include allergies, intolerances, and sensitivities. It is important to differentiate between them to ensure appropriate management and treatment strategies. 

Food allergies are IgE-immune mediated reactions that mount an immediate allergic immune response, associated with mild to severe symptoms like hives, shortness of breath, and anaphylaxis. Food allergies can be diagnosed with a blood test that measures IgE antibodies to specific food proteins. 

Food sensitivities are IgG-immune mediated delayed reactions that can occur up to 72 hours after exposure to a food trigger. Food sensitivities commonly manifest as gastrointestinal symptoms, including diarrhea, but can also cause extraintestinal symptoms, such as headaches, joint pain, and skin rashes. A panel that measures IgG antibodies against food proteins helps to diagnose food sensitivities. 

Food intolerance refers to difficulty digesting or metabolizing certain components of food or food additives. Food intolerances are not immune-mediated and often result from enzyme deficiencies. Tests that can help diagnose food intolerances include the lactose and fructose malabsorption breath tests to diagnose lactose and fructose intolerance, respectively. (27


Functional Medicine Treatment Protocol for Diarrhea

A functional medicine treatment protocol will vary depending on the underlying cause of gastrointestinal dysfunction. Underlying health conditions, such as hyperthyroidism or diabetes mellitus, should be treated promptly. The rest of this article will primarily emphasize a functional medicine approach to treating chronic diarrhea, including dietary modifications and supplements to reduce intestinal inflammation and optimize the diversity and abundance of the gut microbiome.

Therapeutic Diet and Nutrition Considerations for Diarrhea

A bland or BRAT (bananas, rice, applesauce, and toast) diet is generally recommended during acute diarrhea to remove difficult-to-digest and irritating foods that can aggravate acute gastrointestinal symptoms. Staying well hydrated and drinking electrolytes is equally important to prevent dehydration and electrolyte imbalances. (38

For persistent or chronic diarrhea, an excellent place to start treatment is with a gut-healing elimination diet designed to reduce or remove foods that irritate the gut lining and contribute to dysbiosis, heal leaky gut, feed the good gut bacteria, and reduce inflammation. An anti-inflammatory diet, tailored to accommodate specific food allergies, intolerances, and sensitivities, should emphasize whole foods that contain a healthy ratio of complex carbohydrates, unsaturated fats, lean proteins, and fiber. 

Specific foods can be incorporated to help heal the gut naturally with functional nutrition. Probiotic foods, such as kimchi and sauerkraut, contain live cultures of beneficial microorganisms that can help beneficially alter the microbiota's composition and displace pathogenic organisms, enhancing the integrity of the gut barrier and modulating immune activity. Prebiotic foods contain nondigestible compounds that can modulate the composition and activity of the gut microbiota. Examples of prebiotic foods include bananas, onions, and legumes. 

Studies have shown that collagen reduces digestive symptoms, prevents the breakdown of the intestinal lining, and protects the gut from damage by pro-inflammatory molecules. Collagen is found naturally in animal products that contain high amounts of connective tissue. Bone broth is an excellent source of collagen. (15

Soluble fiber absorbs water in the digestive tract, firming stool and its transit through the intestines. Pectin is a soluble dietary fiber in fruits, vegetables, legumes, potatoes, and sugar beets. Substantial evidence supports that pectin has prebiotic effects (promoting a favorable microbiota composition), delays gastric emptying, improves IBS-D, and reduces stool frequency. (28

Supplements Protocol for Diarrhea

The following protocol can be used as a generic template for doctors to implement with their patients as part of a 5R healing protocol. A 5R protocol aims to support and heal the digestive tract by removing offending agents, replacing important digestive enzymes, reinoculating the gut with healthy microbes, repairing the gut lining, and rebalancing gut function with healthy lifestyle habits. Supplements used during a protocol may be dosed simultaneously, or staggered in phases. Treatment protocols should be customized based on the patient's medical history, laboratory findings, and preferences.


Biocidin® is a broad-spectrum formula that combines 18 botanical extracts and essential oils to maintain a healthy microbiome. The botanicals act as natural alternatives to antibiotics and antifungals to correct dysbiotic patterns and modulate the immune system to maintain healthy inflammation levels in the gastrointestinal tract. (3

Dose: 1-2 capsules 2-3 times daily 

Duration: 4-6 weeks


A variety of commercial probiotic products are available. Systematic analyses confirm the efficacy of various probiotic species in treating acute and chronic diarrheal diseases, with improvements noted as soon as the second day of treatment (2, 24). The benefits of probiotics are strain-specific, meaning different strains have different effects and therapeutic potential. Therefore, when selecting a probiotic product, it's important to consider the specific strains in the formula to achieve the desired health outcome. 

Dose & Duration: will vary depending on the chronicity and cause of diarrhea

GI Response

Combination products, such as GI Response by Innate Response, contain a variety of natural ingredients and botanicals that soothe inflammation and promote the healing of the intestinal lining. Ingredients including L-glutamine, aloe vera, and marshmallow root are commonly recommended for celiac disease and IBD, common culprits of chronic diarrhea. (30

Dose: 1 scoop mixed in water twice daily 

Duration: 4-6 weeks

Digestive Enzymes

Supplemental digestive enzymes can replace hydrochloric acid, bile, brush border, and pancreatic enzymes in a deficient state to promote the digestion of food and the absorption of essential nutrients. Digestive enzyme formulas should be based on the patient's needs, often guided through patient-reported history of food intolerances or functional test results. Small studies and case reports have indicated that enzymatic therapy with meals can reduce food-related gastrointestinal symptoms, including diarrhea.

When to Retest Labs

A 5R protocol often takes at least 3-6 months to complete. Repeat labs may be ordered during the process to ensure the patient is meeting specific goals, like eradicating an identified infection, for example. However, repeat labs are generally postponed until after the protocol is finished. Retesting labs may not be required, as improvement in bowel habits and food tolerance can be used to monitor treatment success. 

Learning More About Diarrhea



Diarrheal illness is common, affecting most people at some point during their lives. While diarrhea may be self-resolving, functional medicine helps to support the gut-healing process with nutrition and supplements. Specialty labs measure functional markers of gut health and function to identify underlying causes of secretory and inflammatory diarrhea more thoroughly. These labs help to personalize treatment recommendations for improved health outcomes. 

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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