You've most likely heard of small intestinal bacterial overgrowth (SIBO), but small intestinal fungal overgrowth (SIFO) is gaining attention at a rapid pace for being the culprit of IBS-like symptoms. Since SIFO doesn't respond well to SIBO treatments, this is huge news for the one in five Australians who have irritable bowel syndrome (IBS). Below we will discuss everything you need to know about SIFO including how to treat it.

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Contents:

What Is SIFO?

Understanding the Difference Between SIBO and SIFO

Types of Fungus Involved in SIFO

Symptoms of SIFO

Common SIFO Causes

SIFO Tests: How to Diagnose SIFO

SIFO Treatment: How to Get Rid of SIFO

Final Thoughts on SIFO

What Is SIFO?

As we mentioned, SIFO is an overgrowth of fungus in the small intestine. Originally, this was a larger problem for patients with compromised immune systems. However, research shows that it's also a problem for people with healthy immune systems as well. (1)

Current research shows that 26% of participants who have unexplained gastrointestinal issues had SIFO. These findings encouraged other people to start to consider SIFO as a medical issue in its own right instead of in relation to SIBO. Since traditional SIBO treatments don't work for SIFO, it's important to know which one you have so you can get the proper treatment to get relief from your symptoms.

What's more, SIFO is harder to diagnose because there isn't a lot of research on understanding the role of fungi in your body. Fungi are always present in your gastrointestinal tract. However, pinpointing when it turns from good fungi to the fungi that cause the IBS-like symptoms isn't known.

Understanding the Difference Between SIBO and SIFO

Now that you know what SIFO is, you have to understand the difference between SIBO and SIFO. Unfortunately, they both have similar symptoms, and SIBO is more well-known. This can lead to a lot of misdiagnoses.

The cause of these two GI problems is the biggest thing that differentiates them. SIBO stands for small intestinal bacterial overgrowth. (2) This generally means that your body produces too much bacteria that gets trapped in your small intestine. Another option is that an infection in your small intestine is causing bacteria to build up, and this causes the common symptoms that come with SIBO.

On the other hand, SIFO stands for small intestinal fungal overgrowth. As we touched on, your digestive tract is home to several different fungi, and they help to keep your digestive tract healthy. (3) However, when the fungi colonise and begin to grow out of control, you get the symptoms that come with SIFO.

Another big difference between the two conditions is the treatment options. Traditionally, a rigorous round of antibiotics can help to treat SIBO and get rid of the symptoms. These antibiotics won't work on SIFO, so people who are misdiagnosed may not get the relief from the symptoms with which they present.

Also, physicians widely believe that SIFO will present in people with compromised immune systems, diabetes, HIV, or people who are on long-term steroids more than it will in healthy people. SIBO is common in both people with compromised immune systems and healthy people.

Diagnosing the two different conditions is also where they differ. A popular way to diagnose SIBO is by getting a breath test. This is an accurate way to measure the bacteria count in your body. However, the fungus doesn't present in a breath test, so this isn't an accurate tool to diagnose it. SIFO also typically presents other symptoms than SIBO. For example, stomach upset, gas, bloating, diarrhoea and cramps are common with both infections. However, SIFO may also have other symptoms like fatigue, confusion, or excess ear wax.

Types of Fungus Involved in SIFO

There are several types of fungi found in your gastrointestinal tract, but only a small amount of them are capable of growing and colonising your GI tract. (4) This is good news because it means that there are fewer chances of it growing unchecked and causing the common symptoms that come with SIFO.

1. Candida

One of the main culprits behind SIFO is the yeast family Candida. There are over 20 different species of Candida yeast that are capable of causing an infection. (5) Candida can infect various parts of your body and cause different types of yeast infections. This includes thrush in your mouth or throat, bloodstream infections, skin infections, vaginal yeast infections, and SIFO in your small intestine.

Candida lives in your small intestine, and it helps your body absorb nutrients. It also helps the digestive process along. Drinking a lot of alcohol, having high-stress levels, eating a diet that consists of a lot of fermented foods, or taking an extended course of antibiotics that kills other good bacteria can contribute to candida overgrowth.

2. Galactomyces

A second fungus that is capable of colonising your GI tract is Galactomyces. It is also part of the yeast family, and it can infect multiple areas of your body just like Candida. The main function of this fungus is to help improve your skin's moisture barrier and elasticity, and it has powerful antioxidant effects.

It's also able of colonising and thriving in your GI tract, and this can lead to overgrowth and SIFO symptoms. Galactomyces is one of the most prevalent fungi in stool samples taken from patients suffering from symptoms of IBS. (6) Again, researchers don't understand this fungus’ role in your body that well, but things like being on long-term antibiotics can kill the bacteria that keep Galactomyces in check, and you get an overgrowth.

3. Geotrichum

Geotrichum is naturally found in the digestive tract as well. It's widely associated with the human sputum, feces, and skin. It occurs in between 25% to 30% of every specimen that researchers collect. You can also find it on every continent in the soil.

Under the right conditions, Geotrichum can colonise the GI tract very rapidly. Unlike a lot of fungi, Geotrichum infections are more common in patients with compromised immune systems, like cancer patients and patients with open wounds. (7) These open wounds allow the fungus to go from your skin to your bloodstream and spread from there. It's common in the respiratory tract as well as in the GI tract.

4. Saprochaete

Saprochaete is a fungus that is slightly more uncommon for overgrowth, but you can find it in your GI tract as well. If you give it the correct conditions, it can colonise and grow very rapidly. (8) This is another fungus that is more common in patients with compromised immune systems, but you can find it causing problems in healthy people as well.

This yeast-based fungus lives on your skin as well as in your body. It waits for cuts or abrasions through which to make its way into your bloodstream. (9) It is a weaker fungus, and this is why it is more common in patients with lower good bacteria counts or compromised immune systems.

5. Malassezia

You can find Malassezia on your skin and on animal skin. It's a fungus that is common in opportunistic infections in your body, and it has the ability to colonise and grow very rapidly in your GI tract.

There are three different types of Malassezia fungi, and you can find two of them on and in humans with the third found on animal skin. Common things that can cause the Malassezia fungus to colonise include eating a high-fat diet, having a weaker immune system due to infection or disease, having high amounts of oxidative stress and more.

Symptoms of SIFO

Now that you know the common fungi that can cause SIFO, as well as how it differs from SIBO, we're going to go over classic SIFO symptoms. (10) This will help you get a good idea of which overgrowth or infection you have.

Abdominal Pain

One of the most prominent symptoms of SIFO is abdominal pain. This pain is typically concentrated in the lower abdomen or pelvic area, and it can come and go in waves of pain. You may feel completely fine one hour, and the next hour you could experience sharp or shooting abdominal pain.

Controlled studies showed that patients with compromised immune systems typically experience more prolonged abdominal pain than otherwise healthy individuals. (11) You may also feel pressure instead of pain, and this pressure could be more of a dull ache.

Belching

Belching is a natural way for your body to get rid of excess air from the upper digestive tract. You can swallow excess air by eating too quickly, talking while you eat, drinking carbonated beverages, smoking or habitually sucking on hard candy.

Excess air can also build up in your GI tract if you have a bacterial imbalance that allows fungi to colonise. You may notice that when you belch, you get a slight sense of relief as you expel some of the trapped air. This feeling can go away rather quickly, however, because it'll start to build up again at a rapid pace. You might also notice an unpleasant taste.

Bloating or Fullness

Another more severe SIFO symptom is bloating or feeling full for no apparent reason. (12) Bloating means that your abdominal area feels tight or full, and it's usually full of gas. Since SIFO causes imbalances in your digestive tract, it can cause bloating. Additionally, people who have a condition like IBS are more sensitive to this feeling.

A poor diet or a diet that is rich in fat can be one cause of this feeling. Since certain SIFO fungi thrive on fat and need it to colonise, this could explain why you experience these feelings with a SIFO attack.

Brain Fogginess or Confusion

A common symptom that sets SIFO apart from SIBO is confusion or brain fogginess. This means that people who have SIFO are more prone to experiencing these symptoms. You could momentarily forget why you started to do a task, not remember the date, forget where you placed things or just feel very fatigued and worn out.

One study showed that the participants who had SIFO demonstrated a greater confusion level than the participants that had SIBO. (13) Around 28 out of 30 participants reported that they had difficulty concentrating, poor short-term memory and impaired judgement that lasted between 30 minutes to a few hours.

Diarrhoea

Any time there is something in your body that it doesn't agree with, it tries to get rid of it in any possible way. For a fungal infection in the GI tract, diarrhoea is a common way of doing this.

Most cases of diarrhoea last for a few days, but if your case lasts longer than a few weeks, this is usually a pretty good indication that something is very wrong. This is also one of the symptoms that separate SIFO from SIBO. (14) You usually don't see as much or as prolonged diarrhoea with SIBO. Having an unbalanced diet with high stress can contribute to your GI problems, and it encourages the SIFO fungus to colonise and grow.

Gas and Flatulence

Experiencing symptoms like gas and flatulence are common symptoms of SIFO. This is because your body is trying to get rid of any excess gas or air that results from an infection or imbalance in your digestive tract like a colonisation of SIFO fungi causes. As more and more gas builds up in your GI tract, you could start to feel full, bloated, and uncomfortable. The gas can escape easily through flatulence, and this is another symptom that differs from SIBO because people rarely have this problem when it's a bacterial infection instead of a fungus infection.

Nausea

While nausea does have several causes, a few of the most common ones include motion sickness, migraine, low blood sugar, food poisoning and GI upset. While this isn't necessarily a painful sensation, it is unpleasant. It can even be debilitating, and you'll feel unease or discomfort along with the urge to vomit.

SIFO can wreak havoc on your digestive tract, and this can lead to you feeling nauseous as your body fights to regulate itself. When you throw up, it's not unusual for you to feel better immediately after because your body expelled what it thought was making you feel nauseous.

Common SIFO Causes

What causes SIFO? There are several common things that can make you more vulnerable to SIFO. Understanding what causes it can help you prevent it better because it's better to have preventative measures in place than spend all of the time it can take to diagnose and treat it properly.

1. Excessive Antibiotic Usage

Your body has a host of bacteria that are beneficial to help regulate and maintain your system. There are over 1,000 different bacteria species that have over 1,500 different strains, and all of them are active in your digestive tract at the same time. (15) These bacteria perform several key functions, including helping to break down the food you eat, maintaining the overall balance of your digestive tract and stopping the fungi from colonising.

Antibiotics are useful for fighting bacterial infections. However, antibiotics can't tell the difference between good and bad bacteria. Several studies show that prolonged use of antibiotics can drastically reduce the good bacteria counts in your system as well as the bad bacteria. (16) In turn, the fungi have nothing to keep them in check and stop them from colonising. This is why you generally see more people with compromised immune systems develop SIFO. They're on long-term antibiotics that kill the bacteria in their system.

2. Poor Food Choices

In some western countries, around 35% of people's dietary intake consists of highly processed foods and junk foods. (17) Children between 14 and 18 years old have diets that consist of 41% highly processed foods and junk foods. This sugar intake can have several negative consequences for your health, and it can also make you more prone to SIFO.

Although a high-fat and processed diet may taste good, it gives the Candida fungus a place to colonise because it needs high fat to kick-start the growth cycle. Studies with rats showed that one group that was fed a high-fat diet had a higher colonisation rate than the control group that was fed a lower-fat diet. (18) As Candida fungus is one of the main causes of SIFO, this study outlines why having a healthy and low-fat diet is critical to reducing the chances of fungus colonisation in your digestive tract.

3. Long-Term Usage of Proton Pump Inhibitors (PPIs)

For people who have chronic issues with stomach acid or ulcers like Gastritis, GERD, ulcers or problems with acid reflux, proton pump inhibitors, or PPIs are common long-term medications that they can take to help manage their stomach acid levels. (19) They actually reduce the amount of stomach acid present in your body, and this allows you to better manage your discomfort or symptoms.

Most PPIs are meant for short-term use only, and many people take them longer than the recommended four-week course because you can buy them over the counter. Although long-term use of PPIs won't kill bacteria in your system, it can alter the conditions enough so that strains of bad bacteria and certain fungi can flourish and colonise.

Canadian scientists performed a study with two groups of participants. (20) One group used PPIs on a long-term basis, and the other group didn't use PPIs. They found that the group that used PPIs had a digestive tract that allowed for certain strains of bacteria and fungi to flourish because the PPIs altered the environment enough to make it favourable for colonisation.

4. Dysmotility and Neurological Issues

Dysmotility is a common digestive condition where certain groups of your intestinal muscles don't work as they should or work in sync with one another. (21) This can cause changes in the strength, speed, and coordination of the digestive organs. When this happens, food can get trapped in the intestines, and this can lead to a breeding ground for SIFO fungus. This is especially true if you follow a high-fat diet because certain strains of the fungi feed off of and use fat to colonise.

One study took 150 people who complained of bloating, gas and other gastrointestinal symptoms and tested them for dysmotility as well as SIFO and SIBO. (22) Of these 150 patients, 63% had some form of overgrowth with 40% having SIBO, 26% having SIFO and 34% had a mix of the two. What's more, 53% of the patients had dysmotility or neurological issues, and 43% used long-term PPIs. This allows you to safely draw the conclusion that dysmotility, neurological issues, and long-term use of PPIs can all lead to SIFO fungus overgrowth.

SIFO Tests: How to Diagnose SIFO

Unfortunately, the tests the medical professionals perform to diagnose SIFO are more invasive than the breath test that is so popular for SIBO testing. This is because the fungus that is the main cause of SIFO won't show up on a breath test like SIBO's bacteria will. So, your physicians have to go deeper to get a definitive diagnosis. There are several ways that they can accomplish this, and they may perform more than one SIFO test to be sure.

Small Intestine Aspiration

Your physician will perform an Esophagogastroduodenoscopy (EGD) in an outpatient setting in order to get a small sample of your small intestine and send it back to the lab for a culture to test for fungus growth. (23)

The process starts when you schedule your appointment and arrive. Your physician will give you a drug through an IV to help you relax. You shouldn't remember much of the procedure, thanks to anesthesia. They'll spray a local anesthetic into your mouth to numb the area and insert the small flexible tube with a camera and light on the end into your mouth, down your throat, through your stomach and into the upper portion of your small intestine.

They'll examine the surrounding tissue and take a small biopsy sample to look at under a microscope. The entire SIFO test takes around 20 minutes, and the lab will watch the biopsy for any fungus growth. You'll get the results back within three to four days, but some labs will watch it for up to a week.

Stool Testing

Stool testing is a slightly less invasive way to test for the presence of SIFO. However, you should note that this SIFO test does allow you to see Candida in the stool, so it can also lead to a false positive.

People like this SIFO test because it's largely non-invasive, quick, and easy to perform. Most labs will even let you collect the sample at home. If you start to show signs that you have a problem or an infection in your GI tract, your primary care physician may order a stool test. They may also order more than one over a span of a few weeks to help monitor the fungus levels in your body.

Once your physician orders the test, they typically give you a sample cup to take home and use to collect your stool sample. You simply have to go to the bathroom, collect the sample and bring it back in. You do usually have a time window of two days between collecting the sample and bringing it back to the clinic for the lab to test. However, you do want to double check because some clinics and labs have different requirements for this SIFO test.

Once you bring it back, the lab will analyse it under a microscope. They'll look for the Candida and let you know within a few days if the test was positive or negative.

Blood Antibody Testing

One test that is less invasive than small intestine aspiration and more accurate than stool testing is blood antibody testing. Your physician can make you an outpatient appointment if they believe that you have an overgrowth of Candida.

The lab will draw a blood sample in an outpatient visit and culture it over the span of a few days. They'll take these few days and look for evidence of Candida in your blood. You should know that there is a concern about whether or not this is an accurate SIFO test. One of the main concerns is that this antibody testing doesn't tell you whether or not you have an active Candida infection. It suggests that you may have had an active infection at one point during your life.

Capsules

Going forward, more medical professionals are looking into alternative testing measures for SIFO. They're currently working on capsules that you swallow, and then they sample your GI tract juices every 15 minutes looking for signs of SIFO. Currently, this testing is in its infancy, and you won't see them put to use for another few years.

SIFO Treatment: How to Get Rid of SIFO

If you don't get a concrete diagnosis, your doctor can order a short round of antifungals based on your symptoms. This short-term dosage isn't likely to cause any lasting problems. Also, if the patient responds well to the antifungal medication, it's a good indication that they have SIFO, and you can continue with the SIFO treatment or get more appropriate medications started.

Natural Antifungal Treatments

Many people are not fond of taking medications, and they prefer to take a more natural route. The good news is, that SIFO responds very well to natural antifungal remedies and medications. Natural SIFO treatments also tend to be more broad-ranging, and this helps treat multiple types of fungi that could cause SIFO. However, natural treatments tend to take longer to work, and insurance won't cover the cost.

• Berberine - Berberine is an alkaloid found in several different herbs. (24) It's extracted from the roots and stem bark and put into capsules. This natural treatment has powerful antifungal properties that target Candida yeast and work to stop the colonisation and reduce your symptoms and infection. As a bonus, it also helps control blood pressure.
• Oregano Oil - Oregano oil is another powerful and natural antifungal treatment option. (25) One study had participants with athlete's foot submerge them in a bath of water and oregano oil. They found that the oil killed almost 100% of the fungus at the source. It also has anti-depressant properties.
• Probiotics - Several probiotic strains have been shown to help eliminate SIFO overgrowths. Lactobacillus acidophilus is one of those.

Pharmaceutical Antifungal Treatments

On the other end of the spectrum, we have pharmaceutical antifungal SIFO treatments. These treatment options work quicker than their natural counterparts and insurance will usually cover the cost of these medications. They're more targeted to specific types of fungus, and this makes them more effective at treating SIFO.

• Fluconazole - Fluconazole is a powerful antifungal medication that targets Candida and other fungus strains. (26) It attacks the yeast of fungus and kills it. Additionally, this medication will also work to prevent new growth from happening.
• Nystatin - Nystatin is another powerful antifungal medication that targets a variety of different fungi infections. (27) However, there is some concern that it may break down too quickly in your stomach due to the acid content.

SIFO Diets

In addition to medications to treat SIFO, you can help to prevent ever getting it in the first place by switching your diet. There are several diets geared toward SIFO prevention available, and prevention is always better than diagnosis and treatment.

• SDC - Specific Carbohydrate Diet (SDC) is designed for people with digestive problems and inflammation. This diet only allows for simple sugars and excludes any larger carbohydrate molecules. You eat easily digestible and nutrient-rich foods that help to balance the bacteria in your GI tract. This diet works very well used in conjunction with bone broth, collagen peptides and digestive enzymes.
• FODMAP - FODMAP is an acronym for Fermentable Oligo-, Di-, Mono-saccharides And Polyols. This diet works to introduce short-chain carbohydrates into your diet while reducing the long-chain carbohydrates. The reasoning behind this is that short-chain carbohydrates are easier to digest and break down, and this gives the fungus less to colonise with.
• Elemental - The Elemental Diet is a liquid-based diet. It's a flavoured powder that you mix into water and drink, get it through an IV or through a feeding tube in more severe cases. It's packed with nutrients that help to regulate your digestive system and balance out the bacteria. In turn, the bacteria can keep the fungus in check and help prevent SIFO.

Final Thoughts on SIFO

SIFO continues to gain attention as more and more people discover that they have this digestive tract disorder. We've given you a comprehensive overview including what it is, how it differs from SIBO, what causes it, symptoms, how to diagnose it, treatment options and possible diets that may help to prevent it. You should have a good grasp on whether or not this sounds like something you're experiencing. If you have concerns, contact your physician.

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Editor's note: This article was originally published on December 11, 2018. It was updated on June 15, 2022.