Gut Health Evidence based Evidence Based This article is based on scientific evidence, written by experts and fact checked by experts. Our team of licensed nutritionists and dietitians strive to be objective, unbiased, honest and to present both sides of the argument. This article contains scientific references. The numbers in the parentheses (1, 2, 3) are clickable links to peer-reviewed scientific papers. Everything You Need to Know about SIFO (Small Intestinal Fungal Overgrowth) Medically reviewed by Joe Mather — Written by Dr. Michael Ruscio, DNM, DC onDecember 7, 2019 Written by Dr. Michael Ruscio, DNM, DC on December 7, 2019

Could SIFO be causing your unexplained IBS symptoms?

Could a fungal infection in the small intestines be the cause of your gastrointestinal symptoms and leaky gut?

Recent research at Augustana University found that an overgrowth of fungus in the gastrointestinal tract might be the root cause for more than 25% of IBS patients!

When it comes to gut infections, small intestinal fungal overgrowth or SIFO is the new kid on the block. SIFO was introduced to the medical community in a research paper published in 2015 [1 Trusted SourcePubMedGo to source]. As with any new discovery, there are skeptics. And, of course, more research is needed.

Personally, I think SIFO may prove to be a very important finding when it comes to unexplained gastrointestinal symptoms. I’m glad to see this topic emerging and I am following the research closely.

Most of my readers are familiar with small intestinal bacterial overgrowth or SIBO by now. Our understanding of how to treat SIBO has really evolved in the last few years and it’s helping a lot of patients. But I also see a subset of patients in my clinic who have all of the symptoms of SIBO (gas, bloating, belching, abdominal pain, diarrhea or maybe even constipation) and yet their digestive tests are normal.

I’ve always suspected that something else was wrong in these cases; something that has nothing to do with bacteria.

The symptoms of SIFO and the symptoms of SIBO are identical.

Both conditions involve the symptoms that we associate with IBS or irritable bowel syndrome. But the culprit is completely different: Fungus.

A Fungus Among Us

Fungal infections are known to occur outside the gastrointestinal tract and can cause conditions like athlete’s foot, ringworm, vaginal yeast infections, thrush and more.

When it comes to the gastrointestinal tract, fungal strains (like bacterial strains) are a normal part of the gut ecosystem and not usually a cause for concern. Bacteria and fungi mostly colonize the large intestine; the small intestine is only lightly colonized as it provides a much less hospitable environment. Problems start to occur when heavier colonization takes place in the small intestine and leads to overgrowth.

What happens when there’s an overgrowth in the small intestine?

If it’s an overgrowth of bacteria, you have SIBO

If it’s an overgrowth of fungus, you have SIFO

Those who were negative for SI B O often had SI F O

In a multi-year study of 124 patients with otherwise unexplained gastrointestinal symptoms, more than 25% of the patients were diagnosed with SIFO through endoscopic testing [1 Trusted SourcePubMedGo to source].

Symptoms of SIFO

Belching, bloating, indigestion, nausea, diarrhea, and gas are the digestive issues that are most often found with SIFO.

Unfortunately, these are very common symptoms and this makes diagnosing SIFO via symptoms difficult. It’s common for SIFO patients to see multiple practitioners, endure repeated GI tests and still have no diagnosis.

Treatment for fungal infection does bring dramatic improvement in gastrointestinal symptoms for these patients. Patients also report improvements in:

Joint pain and discomfort

Fatigue and energy levels

Headache

What Causes SIFO?

There are a number of factors that can increase your risk for SIFO:

Excessive use of proton pump inhibitors

Excessive use of antibiotics

Taking immunosuppressant drugs

Diabetes

Ehlers-Danlos syndrome

Motility disorders

Colectomy [ 2 Trusted Source PubMed Go to source

Lack of stomach acid also plays an important role in SIBO and SIFO. Stomach acid production is crucial for gut health. One of the important functions of stomach acid is killing bacteria and fungi before they enter the small intestine. Some people don’t produce enough stomach acid and this increases their risk for SIBO and SIFO.

Some conditions increase the likelihood you have low stomach acid, including:

Autoimmune conditions

Anemia

Being over sixty-five

Chronic use of painkillers or antacids

I want to make a special note about proton pump inhibitors (PPIs).

If you use proton pump inhibitors over long periods of time, you significantly increase the risk of bacterial and fungal infections in your gut [3], [4], [5].

PPIs are designed to lower stomach acid. They play an important role in the treatment of some GI disorders. For example, short-term use of proton pump inhibitors is a very effective treatment for stomach ulcers. But I believe these drugs are overprescribed. Please use proton pump inhibitors with caution.

Testing for SIFO

There are a number of ways to test for bad bugs the gastrointestinal tract. We can do a stool test to identify an overgrowth of pathogenic bacteria like H. pylori, Campylobacter and Salmonella or protozoa like Blastocystis hominis and Giardia. We can use a breath test to identify a SI B O infection. None of these tests are perfect, but they do provide good diagnostic options.

When it comes to SIFO, there are no readily available diagnostic tests.

In the research lab, SIFO tests are done by extracting fluids from the digestive tract with an endoscope. This is a highly invasive procedure and it’s not practical for clinical practice. While there may be some exciting new diagnostic tests on the horizon, for now we must diagnose SIFO based on clinical evidence and empiric treatment.

Clinical Evidence

If a patient has significant digestive issues that correspond with symptoms of SIFO and if testing for other GI infections is negative, we can suspect SIFO.

Empiric Treatment

If SIFO is suspected, the best approach is to go ahead and try an antifungal treatment to see if it works. This is called empiric treatment. If the patient’s digestive issues start to clear up, we can confirm, the diagnosis of SIFO.

Prescription antifungals and natural treatments for SIFO are quite safe. This makes empiric treatment a good choice for SIFO.

Treating SIFO

Antifungal Drugs for SIFO

Standard treatment for SIFO is 3 weeks of antifungal drugs. Fluconazole is the top choice drug because it is specific to candida and its cousins. Alternative antifungal drugs are itraconazole or posaconazole.

Nystatin may not be as effective for SIFO because it appears to get broken down by stomach acid and may not reach the small intestine at an effective dose.

Patients should be aware that these medications can have significant drug interactions, especially if patients are taking medications to control abnormal heart rhythms, blood sugar or anticoagulants.

Natural Treatments for SIFO

In my experience probiotics and herbal antimicrobials like oregano, artemisinin and berberine, can be as effective as antifungal medications. While these natural treatments have not yet been directly studied in the treatment of SIFO, probiotics have shown impressive ability to combat intestinal fungus:

Probiotics are as effective as antifungal drugs:

In a study of 181 infants, the probiotic S. boulardii was as effective as Nystatin (an antifungal medication) in reducing fungal infection . The infants taking probiotics had fewer side effects than the infants taking Nystatin [ 6 Trusted Source PubMed Go to source

. The infants taking probiotics had fewer side effects than the infants taking Nystatin [ They also experienced an increased food tolerance.

Another benefit of herbal antimicrobials is they confer both antibacterial and antifungal action. This is important because research shows that half of patients infected with SIFO also have SIBO [1 Trusted SourcePubMedGo to source].

What’s the Best Dietary Approach for SIFO?

We don’t have any research to directly answer this question. However, I would not advise blindly following a low carb diet because “carbs feed fungus”. Your gut is not that simple. Use whatever diet you feel best on. For some, this will be a lower carb diet. For others this could be low FODMAP or meditearanian diet. An elemental diet is also an option.

The best diet for the host (you) is likely the best diet for the microbiota (the world of bacteria and fungus in your gut). See here for more help finding the best diet for your gut.

Repeating Treatments for SIFO

Some patients have challenging conditions that cause SIFO (and SIBO) to recur. These patients may have an underlying dysmotility (e.g. scleroderma, Ehlers-Danlos syndrome, gastroparesis) or may have had a colectomy.

In these cases, a cyclical approach to treatment may be necessary to keep digestive issues in check and ensure a better quality of life. I prefer using herbal antimicrobials over prescription meds in these cases.

Preventing SIFO

A healthy, balanced diet and high-quality probiotic supplements are usually advisable for good gut health. In addition, it makes sense to address the root causes of SIFO, where possible. This may include:

Taking a digestive acid supplement to increase stomach acid production

Reducing use of acid-lowering medications (antacids, proton pump inhibitors)

Reducing use of antibiotics and immunosuppressant drugs

If you have a condition that causes dysmotility, seek the help of a competent doctor to provide long-term support. Not all doctors recognize the existence of SIFO or even SIBO.

In Summary

If you’ve been struggling with unexplained digestive symptoms, it’s worth investigating to see if SIFO may be the reason. Thankfully, natural SIFO remedies can be trialed safely without requiring testing. Make sure to OK this with your doctor first.