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Everything You Need to Know about SIFO (Small Intestinal Fungal Overgrowth)

Written by Dr. Michael Ruscio, DC on October 17, 2025

Written by Dr. Michael Ruscio, DC on October 17, 2025 — Reviewed by Hannah Wright

• What Is SIFO?|
• Symptoms|
• Causes|
• Testing|
• Treatments|
• FAQ|

If you’ve ever been told your gut tests are “normal” but you still feel bloated, gassy, and miserable—you’re not imagining things.

In my clinic, I often see clients who check every box for SIBO (small intestinal bacterial overgrowth)—gas, bloating, abdominal pain, diarrhea, even constipation—yet their breath tests come back negative. For years, I suspected something else was driving these stubborn cases.

Now we know: Sometimes the culprit isn’t bacterial overgrowth—it’s fungus.

A condition called SIFO (small intestinal fungal overgrowth) causes the same symptoms as SIBO but has a very different root cause. And unless you’re looking for it, it’s easy to miss. The good news? Once it’s recognized, there are safe and effective ways to address it—and that means lasting relief may be closer than you think.

What Is SIFO?

SIFO is a form of dysbiosis, or microbial imbalance. Instead of bacteria overgrowing in the small intestine, fungi dominate—most commonly Candida albicans, but also C. tropicalis, C. glabrata, and others 1.

Doctors generally define SIFO as having more than 1,000 fungal colony-forming units (CFUs) per milliliter of fluid in the small intestine. Normally, a small amount of fungus coexists with beneficial bacteria and immune defenses. But when this balance breaks, fungi can overgrow and cause symptoms 1.

Symptoms of SIFO

SIFO symptoms often mimic other gut disorders, making it hard to recognize. They include 1:

• Bloating and abdominal distension
• Diarrhea (sometimes with mucus)
• Abdominal pain or cramping
• Gas, belching, indigestion
• Fatigue and brain fog
• Mood changes (irritability, anxiety)
• In severe cases, weight loss or nutrient deficiencies

Immunocompromised people may also report chest pain or reflux. Persistent symptoms—especially when antibiotics fail to treat them—are red flags for SIFO.

Because many of these symptoms overlap with IBS (irritable bowel syndrome) and SIBO, SIFO is often overlooked. Many people endure years of symptoms despite “normal” tests before anyone considers fungal overgrowth. In fact, in a multi-year study of 124 people with unexplained gut symptoms, over 25% of those who tested negative for SIBO actually had SIFO 2.

SIFO, SIBO, IBS, & Candida: What’s the Difference?

Confusion is common—these gut conditions look similar, but they aren’t the same. Here’s how they differ:

• SIFO: Overgrowth of fungi in the small intestine. Symptoms: bloating, gas, diarrhea, abdominal pain, fatigue, mood issues. Diagnosis is difficult since no easy clinical test exists.
• SIBO: Overgrowth of bacteria in the small intestine. Symptoms mimic SIFO but can be detected via breath test.
• IBS: A functional gut disorder with bloating, pain, and altered bowel habits (constipation or diarrhea, or both). IBS doesn’t always have a clear microbial cause, but SIBO or SIFO may be a hidden driver in some people with IBS.
• Candida Overgrowth: Candida is a fungus that occurs naturally on the skin and in the gut, mouth, penis, and vagina. Too much Candida commonly causes yeast infections or oral thrush. It can also overgrow and cause problems in the large intestine, but that isn’t the same as SIFO. SIFO means there’s too much Candida growing specifically in the small intestine—not in the large intestine or other parts of the body.

What Causes SIFO?

The following factors can allow fungi to thrive in the small intestine 1:

1. Antibiotics: These drugs kill off protective bacteria, giving fungi an advantage.
2. Proton pump inhibitors (PPIs): Often used as GERD treatments, these reduce stomach acid, allowing fungi to grow.
3. Immune suppression: Conditions like diabetes or medications weaken immune defenses.
4. Biofilms: Slimy shields protect fungi from antifungals and immune attack.
5. Morphological switching: Candida can shape-shift—spreading as yeast or invading tissue as branching strands of fungus called hyphae.
6. Microbe interactions: Beneficial microbes like Lactobacillus suppress fungi, while pathogens like E. coli may promote them.

Certain risk factors can tip the balance in your gut and make fungal overgrowth more likely. The most common risk factors for SIFO include 1:

• Frequent or long-term use of PPIs 
• Antibiotics, which disrupt healthy gut balance
• Immunosuppressant drugs
• Diabetes
• Motility disorders (when food and waste don’t move through the gut efficiently)
• Connective tissue disorders like Ehlers-Danlos syndrome and scleroderma 3
• A history of GI surgery, such as colectomy

The Role of Stomach Acid

One of the most important defenses your gut has is stomach acid. It helps kill off bacteria and fungi in your food before they reach your small intestine. But if you don’t make enough stomach acid, you’re more vulnerable to SIFO.

Low stomach acid can happen for many reasons, including 4:

• Autoimmune conditions: Pernicious anemia can damage stomach cells and reduce acid production.
• Long-term acid-suppressing drugs: Extended use of proton pump inhibitors (PPIs) can lower stomach acid.
• H. pylori infection: This common stomach bacterium can temporarily reduce acid and may contribute to cancer risk.
• Gastric bypass surgery: This procedure alters stomach function and can reduce acid output.
• Rare tumors (VIPomas): These can trigger diarrhea and reduce potassium levels and stomach acid.
• Hypothyroidism: Low thyroid function can decrease stomach acid.
• Radiation therapy to the stomach: Radiation can damage acid-producing cells in the stomach.
• Gastric cancer: Cancer of the stomach is sometimes associated with reduced or absent stomach acid.

Preventing SIFO

The best way to prevent SIFO is to support your gut’s natural defenses by:

• Supporting healthy stomach acid (with betaine HCl supplements, if needed)
• Using acid-lowering drugs cautiously—long-term PPI use increases infection risk
• Limiting unnecessary antibiotics or immunosuppressants
• Working with a skilled clinician if you have a motility disorder or structural gut issue

Simple steps like eating a balanced diet and using a high-quality probiotic can also help you maintain a healthy gut environment.

How Do You Test for SIFO?

For many gut conditions, testing is straightforward.

• Stool tests can spot harmful bacteria like H. pylori or parasites such as Giardia.
• Breath tests are commonly used to detect SIBO.

SIFO is different. Right now, there’s no simple, non-invasive test available. In studies, doctors diagnose SIFO by taking fluid samples directly from the small intestine with an endoscope—but that’s far too invasive for routine use 1.

So, in practice, SIFO is diagnosed based on:

1. Clinical clues—IBS-like symptoms with no other explanation
2. Treatment response—trying an antifungal (called empiric treatment) and seeing if symptoms improve

The good news is that both antifungal medications and natural options (like probiotics or herbal antimicrobials) are generally safe for treating suspected SIFO. Treating based on symptoms and experience is the most practical path for now.

Treating SIFO: What Really Works

Because SIFO is complex and often overlaps with SIBO, treatment usually requires a layered approach 1. At the clinic, we follow this general protocol:

• Antifungal medications like nystatin (works locally in the gut) or fluconazole (works throughout the body) can directly lower the fungal load.
• Herbal antifungals (like oregano oil, garlic, berberine, and caprylic acid) are gentler and less likely to cause antibiotic resistance 5.
• Probiotics (especially Lactobacillus and Saccharomyces boulardii) can help crowd out fungi and restore balance.
• Diet changes—reducing refined sugar and processed carbs—can starve fungus of its primary fuel.
• Addressing root causes—like reducing unnecessary antibiotics, improving gut motility, and managing stress—can help prevent relapse.

These foundations are essential—to show you a more structured version of it, I’ll outline the practical, step-by-step treatment framework we use in the clinic.

Our Candida protocol is an effective, clinically tested framework for managing fungal overgrowth. It focuses on building health from the ground up instead of jumping straight into antifungal therapy.

Step 1: Diet First

Instead of extreme carb restriction, we emphasize a balanced Candida Diet, with these rules:

• Eat non-starchy vegetables, leafy greens, clean proteins, healthy fats, and low-sugar fruits.
• Limit processed sugar, refined carbs, and alcohol.
• Moderate amounts of fruit, whole grains, and potatoes are allowed, which makes the plan sustainable 6.

For a detailed food list, download our free Candida Diet Guide.

Other gut-friendly diets, like a Paleo Diet or Low FODMAP Diet, can also help if symptoms persist.

Step 2: Lifestyle Reset

Daily movement and stress management can support gut motility and immune balance.

• Exercise—even if you start with a 10-minute daily walk—can improve microbiome health  7.
• Stress reduction techniques (breathwork, meditation, yoga, or time in nature) may prevent stress-related immune suppression that allows Candida to thrive 8.

Step 3: Probiotics

We use a three-part probiotic protocol:

• Lacto/bifido blends (strengthen the gut barrier and immune signaling)
• Saccharomyces boulardii (a beneficial yeast that competes against Candida)
• Soil-based Bacillus species (boost microbial diversity)

Together, these categories are more effective than single strains alone 9.

Step 4: Targeted Antimicrobials

Once steps 1–3 have solidified the foundation of a healthy gut, we layer in herbal antimicrobials. Our Biota-Clear protocol uses two phases:

• Phase 1 (Oregano oil): breaks down fungal biofilms, reduces inflammation, and inhibits yeast growth.
• Phase 2 (Berberine, olive leaf, wormwood, black walnut, artemisinin): gives broad-spectrum support that reinforces gut health and helps prevent recurrence.

These are often better tolerated than prescription antifungals and less disruptive to good microbes 10.

Step 5: Additional Supports (if needed)

For stubborn or recurrent cases, we sometimes add:

• MCT oil: antifungal fat from coconut that starves Candida while fueling the body 11 12
• Prebiotics: reintroduced carefully to strengthen beneficial bacteria and long-term balance 13 14
• Elemental diet (short-term): liquid nutrition that starves overgrowth while calming the gut 15

As SIFO clears, it’s not uncommon to feel temporary “die-off” symptoms like fatigue, headache, brain fog, skin issues, digestive upset, or mood swings. These usually last only a few days and are a sign the body is getting rid of the overgrowth. 

If symptoms feel too strong, we coach people to slow down the protocol, stay hydrated, rest, and use simple supports like lemon water, curcumin, or activated charcoal. The goal isn’t to push through suffering—it’s to move at a pace the body can handle.

What if SIFO Keeps Coming Back?

For some people, SIFO isn’t a one-time problem. Conditions like motility disorders (e.g., gastroparesis, scleroderma), connective tissue disorders (like Ehlers-Danlos), or prior gut surgery can make recurrence more likely.

In these cases, a cyclical treatment approach—rotating probiotics or herbal antimicrobials—may be needed to keep symptoms under control and improve quality of life. For long-term management, we often lean on herbal antimicrobials since they can be used safely over time.

FAQs About SIFO

Is SIFO the same as Candida?
Not exactly. Candida is a common fungus that can overgrow in many areas of the body, causing non-SIFO conditions like genital yeast infections or oral thrush. But when Candida overgrows in the small intestine, it is SIFO.

Can you have both SIBO and SIFO?
Yes. In fact, one study found that about a third of 94 people with small intestinal overgrowth had both SIFO and SIBO 16, which may explain why some people don’t improve with antibacterial treatment alone.

Can SIFO cause symptoms outside the gut?
Yes. People with SIFO sometimes report fatigue, brain fog, irritability, anxiety, or depression in addition to digestive symptoms.

Does diet alone cure SIFO?
There’s no evidence that you can fully resolve SIFO with diet alone. However, trying a Candida diet or finding another diet that supports your gut—such as Paleo or low FODMAP—may make your symptoms easier to manage.

Can probiotics make SIFO worse?
This is a common concern. But research suggests that certain probiotics, especially Saccharomyces boulardii, may actually reduce fungal overgrowth and improve the ability to tolerate food 1.

How long does it take to treat SIFO?
Prescription antifungal treatment usually lasts about 3 weeks, while natural approaches may take longer and sometimes need to be repeated if risk factors aren’t corrected.

Can SIFO come back?
Yes. If the underlying cause—like low stomach acid or a motility disorder—isn’t addressed, recurrence is common. In these cases, people may need cyclical or ongoing support.

The Bottom Line

SIFO is an underrecognized cause of chronic digestive symptoms that often mimics SIBO or IBS. While testing options remain limited, a targeted, step-by-step approach—starting with diet, lifestyle, and probiotics, and layering in antifungal support when needed—can make a meaningful difference.

In my clinic, we’ve seen many patients finally turn the corner once fungal overgrowth was identified and properly treated. By addressing underlying factors like low stomach acid, poor motility, and frequent antibiotic use, it’s possible to restore balance and reduce the chance of relapse.

If you’ve tried SIBO or IBS treatments without lasting relief, our clinical team can help you get to the root cause and find a plan that truly works for your body. Learn more about working with our clinic. 

With the right guidance, most people can calm their gut, regain energy, and finally move past the cycle of bloating, fatigue, and food frustration that SIFO causes.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.