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A Functional Medicine Small Intestinal Fungal Overgrowth (SIFO) Protocol: Specialized Testing, Therapeutic Diet, and Supplements

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A Functional Medicine Small Intestinal Fungal Overgrowth (SIFO) Protocol: Specialized Testing, Therapeutic Diet, and Supplements

Small intestinal fungal overgrowth (SIFO) is characterized by an overgrowth of fungi within the small intestine. While conventional treatments involving antifungal medications and dietary modifications are commonly prescribed, there is growing interest in exploring alternative approaches to manage SIFO. This article delves into the potential of functional medicine to successfully treat SIFO. By considering the underlying causes and individualized patient factors, functional medicine SIFO protocol offers a holistic approach to treatment, focusing on restoring gut health and rebalancing the body's systems. 


What Is Small Intestinal Fungal Overgrowth (SIFO)?

Small intestinal fungal overgrowth (SIFO) refers to an abnormal proliferation of fungi, primarily Candida species, within the small intestine. Normally, the small intestine contains a small number of fungi; however, when the balance of microorganisms in the gut is disrupted, fungi can multiply and grow unchecked. Research suggests that Candida species, such as Candida albicans, are responsible for 97% of SIFO cases. (26

SIFO can lead to inflammation, damage to the intestinal mucosa, and compromised nutrient absorption. The presence of SIFO may also impact the immune response and disrupt the gut-brain axis, contributing to symptoms such as abdominal discomfort, bloating, and cognitive issues. (27

SIFO Symptoms

The symptoms of SIFO can vary and may overlap with other digestive disorders. In fact, studies suggest SIFO is found in about 25% of people with previously unexplained gastrointestinal symptoms, such as those that occur with irritable bowel syndrome (IBS). Common SIFO symptoms include bloating, gas, belching, indigestion, abdominal discomfort, nausea, diarrhea, and constipation. (12, 14)  

Small intestinal inflammation and increased permeability, known as leaky gut, commonly manifests as the following symptoms: 

  • Fatigue
  • Joint pain
  • Headaches
  • Brain fog
  • Mood imbalances
  • Food intolerances

SIFO often does not occur alone. When fungal overgrowth occurs in the gastrointestinal tract, it is common for overgrowth to appear on other sites of the body, too, resulting in symptoms like (27):

  • Itchy skin rashes, often occurring in skin folds
  • Vaginal infections: vaginal itching/burning and white or yellow cottage cheese-like discharge
  • White patches on the tongue (oral thrush) 
  • Urinary tract infections (UTIs)
  • Yellowing and thickening of fingernails and toenails 

What Causes SIFO?

The etiology of SIFO involves the disruption of the normal gut microbiota, called dysbiosis, allowing fungi to overgrow in the small intestine. Multiple factors can cause dysbiosis. Prolonged or frequent use of antibiotics, which disrupts the natural balance of bacteria in the gut, is a significant risk factor. Other medications that increase the risk of fungal overgrowth include steroids and proton pump inhibitors (PPIs). (23

A weakened immune system, as seen in individuals with chronic infections, autoimmunity, diabetes, or undergoing immunosuppressive therapy, can also contribute to SIFO. (23)

Diets high in sugar, refined carbohydrates, processed foods, and alcohol provide an optimal environment for fungal overgrowth. High glycemic diets also increase the risk of diabetes, further contributing to a dysregulated immune system and increased risk of infection. (27

Certain conditions that slow intestinal motility can contribute to SIFO. Causes of slowed intestinal motility include Ehlers-Danlos syndrome, gastroparesis, hypothyroidism, a sedentary lifestyle, and gastrointestinal surgeries. (26

Functional Medicine Labs to Test for Root Cause of SIFO

The gold standard for diagnosing SIFO is a small bowel aspirate, which involves inserting an instrument through the mouth and into the first portion of the small intestine. From there, fluid is collected and analyzed for fungal overgrowth. Given this procedure's cost and invasive nature, specialty labs are often used as first-line diagnostics in clinical practice instead. Functional medicine doctors often order the following labs to diagnose SIFO and identify its underlying causes.

Comprehensive Stool Test

A comprehensive stool analysis measures multiple biomarkers that reflect overall gut health and thoroughly evaluates the health and balance of the intestinal microbiota, including both bacteria and fungi. Stool culture and PCR testing methods help to identify the fungal species responsible for SIFO. In addition, sensitivity testing on the identified pathogen(s) determines the antifungal agents that will most effectively treat the infection.

Candida Antibodies

Since Candida spp. are the most common type of fungus responsible for SIFO, another testing option for ruling in Candida albicans infection is a serum Candida profile, which measures IgA, IgG, and IgM antibodies that are produced by the immune system in response to a Candida albicans infection.

Diabetes Panel

A diabetes panel includes six biomarkers associated with dysglycemia and diabetes. This panel can screen for hyperglycemia, insulin resistance, and diabetes to rule out high blood sugar as an underlying cause of fungal overgrowth. 

Functional Medicine Labs That Can Help Individualize Treatment for SIFO

The following are labs to consider ordering patients with SIFO to help personalize and increase the efficacy of holistic treatment plans. 

SIBO Breath Test

SIFO shares similarities with small intestinal bacterial overgrowth (SIBO), an overgrowth of bacteria in the small intestine. In some cases, SIBO and SIFO can coexist. Performing a SIBO breath test can be helpful to better understand the microbial ecosystem within the small intestine to guide treatment and enhance clinical outcomes.

Leaky Gut Panel

A leaky gut triggered by SIFO or other dysbiotic patterns can contribute to uncomfortable symptoms. A leaky gut panel can detect the presence of intestinal permeability, helping to guide treatment recommendations. This panel can also track treatment progress, as leaky gut should resolve as SIFO is eliminated and the intestinal barrier is restored.

Micronutrient Panel

SIFO and leaky gut may cause nutrient malabsorption, so a micronutrient panel can be beneficial to assess the patient's nutritional status. These results will reveal deficiencies or other nutritional imbalances, helping to guide specific dietary and supplemental recommendations. 


Conventional Treatment for SIFO

Azole antifungal medications are the conventional mainstay for treating SIFO and other fungal infections. Fluconazole and itraconazole are two commonly prescribed antifungal medications.

Nystatin is an alternative antifungal agent commonly prescribed by functional medicine doctors for treating SIFO because it is not absorbed into the bloodstream and, therefore, has a lower side effect profile. 

Functional Medicine Treatment Protocol for SIFO

A functional medicine approach to treating SIFO includes eliminating fungal overgrowth, alleviating associated symptoms, restoring the balance of the gut microbiota, and addressing underlying causes of SIFO to prevent future recurrences.

Therapeutic Diet and Nutrition Considerations for SIFO

Dietary approaches to dysbiosis and gastrointestinal symptoms should be individualized based on the patient's lab work and food tolerance. However, an Candida diet provides a good framework for patients with SIFO because it is designed to minimize foods that promote Candida, or other fungal, overgrowth while focusing on foods that support a healthy gut environment. Here are the fundamental principles of the Candida diet:

Avoid Sugar

Candida feeds on sugar, so it is important to eliminate or greatly reduce the consumption of refined sugars, high-fructose corn syrup, and sugary foods and beverages. This includes candies, cakes, cookies, soda, and fruit juices. (10

Limit Carbohydrates

Carbohydrates, especially refined carbohydrates, can break down into sugar, increase blood sugar, and promote fungal growth. Limiting high-carbohydrate foods such as white bread, pasta, rice, and potatoes is advised. Instead, choose complex carbohydrates from sources like whole grains, legumes, and non-starchy vegetables. (10

Include Lean Proteins

To support a balanced diet, lean proteins such as poultry, fish, eggs, and plant-based protein sources like legumes and tofu can be consumed. Protein helps maintain satiety and build muscle, important for preventing insulin resistance and managing diabetes. (10

Emphasize Non-Starchy Vegetables

Non-starchy vegetables are low in sugar and high in fiber and can support a healthy gut environment. Cruciferous vegetables, leafy greens, and asparagus are examples of non-starchy vegetables that can be included in the diet. (10

Probiotic Foods

Incorporating probiotic-rich foods, such as yogurt with live cultures, can help restore beneficial gut bacteria. While fermented foods are good probiotic sources, they contain yeast and can potentially worsen Candida overgrowth. Fermented foods and foods containing mold, including alcohol, vinegar, cheese, soy sauce, sauerkraut, some types of nuts, and certain condiments, should be eaten in moderation or avoided entirely if identified as a dietary trigger. (10

Supplements Protocol for SIFO

The following is a sample protocol that uses natural supplements to treat SIFO. Supplement protocols should be individualized based on the patient's medical history and fungal sensitivity testing.


CandidaStat® by Vitanica combines botanical herbs and vitamins to create a comprehensive antifungal and immune-supportive formula. Caprylic acid has antifungal properties and helps to break down biofilms, which can contribute to treatment resistance. Allicin, the active constituent of garlic, exhibits antifungal properties through multiple mechanisms. Berberine has broad antimicrobial activity and can also help repair the gut lining through its anti-inflammatory and mucosal healing effects.

Dose: 3 capsules three times daily

Duration: 6 weeks


Probiotics are living microorganisms beneficial to the host's health upon administration of sufficient doses. Research strongly supports the antifungal properties of Lactobacillus and Bifidobacterium probiotics by inhibiting pathogenic fungal growth and the formation of fungal biofilms.

Dose: at least 8 billion CFU daily

Duration: 6 weeks

Saccharomyces boulardii 

Saccharomyces boulardii is a beneficial yeast shown to be as effective as nystatin in reducing fungal colonization. S. boulardii combats Candida overgrowth by breaking down protective biofilms and displacing Candida in the intestinal mycobiome. (27

Dose: 5 billion CFU daily

Duration: 6 weeks

When to Retest Labs

A standard course of natural antifungal therapy is at least six weeks; at this point, follow-up is warranted to determine whether the treatment was successful. Monitoring symptom improvement or repeating fungal testing (i.e., stool, antibody testing) can both be appropriate to gauge treatment efficacy.



A functional medicine approach to treating small intestinal fungal overgrowth considers individual factors contributing to this dysbiotic condition. An individualized treatment plan based on the patient's unique circumstances and lab results includes targeted supplementation that eliminates yeast, reestablishes a healthy intestinal microbiota, and addresses root causes to prevent future recurrence. The protocol explained in this article can be used as a template to base effective SIFO treatment protocols in clinical practice.

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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