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Navigating the Complexities of Fungal Overgrowth

SIFO | Dr. Koji Aoki | Keystone Total Health | Functional Medicine | Columbia, TN

Small intestinal fungal overgrowth (SIFO), was discovered by Dr. Satish Rao a Gastroenterologist who published many articles that explained that SIFO can be a root cause of unexplained GI symptoms. SIFO, delineates a scenario where fungi, typically benign gut residents, grow exuberant.

Ordinarily, candida coexists harmoniously in our digestive tract alongside the diverse array of bacteria that constitute the microbiome. However, when an overabundance occurs, it may inflict harm upon the intestinal lining or engage in prolonged skirmishes with the resident bacterial population. This prolonged conflict can deplete vital resources, ultimately leading to a compromised immune system and a further proliferation of candida.

How Do I Know if I Have it?

There are many ways that you could know if you have SIFO. The symptoms of Small Intestinal Fungal Overgrowth (SIFO) is very similar to Small Intestinal Bacterial Overgrowth (SIBO). If a patient has either one of these conditions that may experience abdominal pain or discomfort, bloating, constipation, diarrhea, fatigue and pain due to nutritional deficiencies. However, in SIFO there are many external symptoms like:

  • Thrush

  • Dandruff

  • Brain Fog

  • Bloating

  • Eczema and Psoriasis

  • Toe/fingernail lifting up (Onycholysis)

  • Ringworm

    • Jock Itch (Tinea cruris)

    • Athletes Foot (Tinea pedis)

    • Onychomycosis – fungal nail infection –(Tinea unguium)

    • Scalp Ringworm (Tinea capitis)

  • Vaginal Yeast Infections

  • Itching Ears

  • Sugar Cravings

How Does Fungus Grow in the Body?

In a healthy gut, there are several fungal species that coexist harmoniously with other

microorganisms, including bacteria. Some of the common fungal species found in a balanced and healthy gut microbiome include:

  • Candida albicans: In moderate amounts, this yeast is a natural part of the human microbiome, residing in the digestive tract. It plays a role in nutrient absorption and helps prevent harmful bacteria from overgrowing.

  • Saccharomyces cerevisiae: Also known as baker's yeast, this fungus is often used in baking and brewing. In the gut, it contributes to the fermentation of carbohydrates and supports the production of certain vitamins.

SIFO | Mold Illness | Dr. Koji Aoki | Keystone Total Health | Functional Medicine | Columbia, TN
  • Aspergillus niger: This fungus is found in small amounts in the environment and can also be present in the digestive tract. It contributes to the breakdown of plant material and the production of various enzymes.

  • Penicillium spp.: This genus of fungi includes various species, some of which are found in small amounts in the environment. They contribute to the decomposition of organic matter and can produce secondary metabolites with potential health benefits.

  • Cryptococcus spp.: These yeasts are typically harmless in healthy individuals. However, they can potentially cause infections in individuals with compromised immune systems.

  • Geotrichum spp.: These fungi are commonly found in soil, water, and dairy products. They can also be part of the normal gut microbiota.

  • Malassezia spp.: These yeasts are commonly found on the skin and in the gut. They are usually harmless but can cause skin conditions in some individuals.

With a bad environment, as Biological Medicine likes to call it – changing the guts natural terrain - many of these fungal species can get outplaced, and problematic species like these listed below can overgrow.

  • Candida albicans: When it overgrows, it can lead to infections and disrupt the balance of the gut microbiota.

  • Candida tropicalis: This species, when present in excess, can contribute to fungal overgrowth-related conditions.

  • Candida glabrata: Similar to other candida species, overgrowth of C. glabrata can lead to infections and digestive disturbances.

  • Saccharomyces cerevisiae (pathogenic strains): While typically harmless, some strains of this yeast can become pathogenic in certain conditions.

What Factors Change our Gut’s Environment?

Certain pharmacological drugs inadvertently usher in a steep decline in stomach acid levels. While this may initially appear advantageous, it paves the way for SIFO. With reduced stomach acid, our natural defense against fungal intruders is compromised, granting them permission to multiply and sow discord. These medications are:

  • Antacid (Alka Seltzer)

  • Proton pump inhibitors (PPIs): Prilosec (Omeprazole), Nexium (Esomeprozole), Prontonix (Pantoprazole)

  • H2 blockers: Zantac (Ranitidine), Pepcid (Famotidine), and Tagamet (Cimetidine) are used conventionally to treat GERD (Gastro-Reflux Esophageal Disease).

All three of these are used as the Standard of Care to reduce symptoms of Grastro-Esophageal Reflux Disease (GERD). Even though they reduce your symptoms they increase your risk of developing dysbiosis (2). A study published in Current Gastroenterology Reports found that 26% and 25.3% of a series of patients with unexplained GI symptoms had SIFO and small intestinal dysmotility and the use of PPIs has been implicated (3).

Antibiotics: The Double-Edged Sword

SIFO | Dr. Koji Aoki | Keystone Total Health | Functional Medicine | Columbia, TN

Antibiotics, omnipresent tools in our armamentarium against infections, possess a dual nature. While they valiantly vanquish harmful bacteria, they may inadvertently neglect the beneficial ones. This disruption to the gut's delicate equilibrium can give rise to a fungal insurgency.

A study featured in the European Journal of Gastroenterology & Hepatology approximates that about 30% of patients who've undergone antibiotic treatments may develop SIFO. This figure, undoubtedly, is of substantial consequence and highlights the nuanced impact of antibiotics.

Estrogen Dominance and the Influence of Oral Contraceptives

Let us now direct our focus towards estrogen and oral contraceptives. In instances of estrogen dominance, where the balance between estrogen and progesterone tilts, the stage is set for fungal proliferation. Additionally, oral contraceptives can disturb hormonal equilibrium, providing a fertile ground for SIFO to flourish.

A study in the American Journal of Gastroenterology revealed that women on oral contraceptives face a 1.7 times higher risk of developing SIFO compared to those who abstain. This statistical finding underscores the significance of hormonal balance in the context of gut health.

The SAD Saga: The Standard American Diet

The Standard American Diet is laden with refined carbohydrates, it lays out a lavish feast for fungi. Just as a shipwrecked sailor craves fresh water, SIFO thrives on the sugars and starches that abound in this diet. Research indicates that individuals with high sugar consumption face a significantly heightened risk of developing SIFO. The message is unequivocal: to maintain gut flora harmony, we must steer clear of this perilous dietary trajectory.

Finding a Diagnosis

Esophagogastroduodenoscopy (EDG)

A gastroenterologist conducts a diagnostic procedure involving an endoscopy. During this examination, a sample of liquid from the small intestine, referred to as a small bowel aspirate, is collected and cultured. If the culture exhibits an elevated presence of candida beyond a designated threshold, a diagnosis of SIFO may be confirmed. Subsequently, medical professionals can delve deeper into the sample to identify the precise strain of fungi or yeast, as well as prescribe the specific treatment regimen required.

SIFO | Dr. Koji Aoki | Keystone Total Health | Functional Medicine | Columbia, TN

Blood Test

You can check the blood for Candida albicans (yeast) antibodies (IgG, IgM, IgA). Beta-alanine, which is a byproduct of candida can be elevated with patients who have SIFO. Secretory IgA will be low with chronic SIFO. This is because the body uses secretory IgA to remove Candida from itself. D-arabinitol, a waste product of SIFO, can also be examined.

Stool Sample

Other labs offer a stool test which includes a qPCR DNA analysis of a stool sample. It is said that candida can continue growing while the stool sample is being transported, making a false-positive. However, in my clinical experience I have seen this as a very reliable source.

Chosing a Natural Approach

Before we dive into the realm of herbs, let's first understand the basics of the antifungal diet. This dietary approach is designed to starve off the fungi that may have overgrown in your system. It emphasizes whole, unprocessed foods while limiting or eliminating sugars, refined carbohydrates, and yeast-containing products. By depriving fungi of their preferred fuel, this diet lays the groundwork for a balanced and thriving gut ecosystem.

Can Have:

  • Uncured Bacon

  • Egg

  • Grass Fed Meat

  • Grass Fed Butter

  • Cheese if tolerated

  • Pain Greek Yogurt

  • Roasted Nuts

  • Broccoli

  • Asparagus

  • Zucchini

  • Onions

  • Carrots

  • Kale

  • Spinach

  • Romaine/Other Salad Greens

  • Cilantro

  • Avocado

  • Tomato

  • Green Apple

  • Mixed Berries

  • EVOO

  • Cinnamon


SIFO | Dr. Koji Aoki | Keystone Total Health | Functional Medicine | Columbia, TN
  • Starchy vegetables (Potatoes, Cassava, Parsnips, Sweet Potatoes, Sweetcorn)

  • Beans

  • Potato

  • Yeast and Fungal Based Products (Brewer’s/Baker’s Yeast)

  • Fermented Foods (Kombucha, Alcohol, Kimchi, Sauerkraut)

  • Fruits (All Fruits except the ones listed above)

  • Grain

  • Added sugars high fructose corn syrup, honey, maple syrup, agave

  • Dairy

The Power of Antifungal Herbs

  • Oregano: The Mighty Warrior

Oregano, beyond being a flavorful addition to dishes, boasts potent antifungal properties. Its active component, carvacrol, has been shown to combat a wide range of fungi, making it a formidable ally in your antifungal arsenal.

  • Garlic: Nature's Antibiotic

Garlic has long been celebrated for its immune-boosting and antifungal properties. Allicin, a key compound in garlic, is known to exhibit powerful antimicrobial effects, making it an excellent addition to your antifungal diet.

  • Coconut Oil: Nature's Elixir

Coconut oil contains caprylic acid, a fatty acid known for its ability to penetrate the cell walls of fungi, disrupting their growth. Incorporating coconut oil into your cooking or enjoying it in its raw form can provide valuable support in your antifungal journey.

  • Pau d'Arco: The Rainforest Healer

Derived from the inner bark of a South American tree, pau d'arco is revered for its antifungal and immune-boosting properties. It contains lapachol, a compound known for its potent antifungal effects.

  • Berberine: The Golden Extract

Found in various plants like Oregon grape and goldenseal, berberine has shown promise in combatting a wide range of fungi. Its multifaceted benefits also extend to blood sugar regulation and immune support.

  • Saccharomyces boulardii: Yeast Fighter

Researchers have found that Saccharomyces boulardii to be effective at getting rid of fungi. This yeast actually displaces other problematic yeast that is found in our gut. They found that when this probiotic was used with infants there were fewer side effects than some antifungals. (4)

Incorporating Antifungal Herbs into Your Diet

Now that we've explored the antifungal prowess of these herbs, let's discuss how to seamlessly integrate them into your meals:

  • Herb-Infused Oils: Create flavorful, antifungal-infused oils by steeping herbs like oregano or garlic in olive or coconut oil. Drizzle over salads or use for cooking to elevate both flavor and health benefits.

  • Herbal Teas: Brew teas using antifungal herbs like pau d'arco or berberine-containing plants. These warming concoctions not only offer a comforting ritual but also provide a therapeutic boost.

  • Fresh Herb Additions: Incorporate fresh herbs like oregano and garlic into your cooking for a burst of flavor and antifungal support. They work wonderfully in sauces, soups, and stir-fries.

  • Supplemental Support: Consider herbal supplements, especially if you find it challenging to incorporate these herbs into your daily meals. When I work with my patients, I customize their own herbal blends based on their own body, so that they can better fight off this fungal overgrowth.

Ending Thoughts

After an in-depth exploration of Small Intestinal Fungal Overgrowth (SIFO) and its intricate interplay with contributing factors, we find ourselves equipped with valuable insights. This newfound knowledge becomes our compass, guiding us towards a path of improved health and freedom from fungal overgrowth.

As we navigate this terrain, it becomes evident that a balanced diet and avoidance of the factors that change our gut terrain is best for our overall gut health. These measures work in tandem, reinforcing our defense against potential overgrowth.

In this journey, let wisdom be your guide, and let each choice be a step towards a more vibrant and balanced state of well-being. Remember, with informed decisions and proactive health practices, we forge a path towards a healthier, fungus-free future.

SIFO | Dr. Koji Aoki | Keystone Total Health | Functional Medicine | Columbia, TN

By Dr. Koji Aoki DC


Hsu M, Safadi AO, Lui F. Physiology, Stomach. [Updated 2023 Jul 17]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from:

Erdogan, A., Rao, S.S.C. Small Intestinal Fungal Overgrowth. Curr Gastroenterol Rep 17, 16 (2015).

Demirel, Gamze, et al. “Prophylactic Saccharomyces Boulardii Versus Nystatin for the Prevention of Fungal Colonization and Invasive Fungal Infection in Premature Infants.” European Journal of Pediatrics, U.S. National Library of Medicine, 24 May 2013,


The content provided on this blog is intended for informational purposes only. It is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your physician or other qualified health provider with any questions you may have regarding a medical condition.

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