SIFO – Small Intestine Fungal Overgrowth Symptoms and Treatment

small intestine fungal overgrowth

Is SIFO or Small Intestine Fungal Overgrowth Smarter Than a Lab Test?

For many years now, patients have been coming in to the office with digestive symptoms and yet all of their “advanced” lab tests come back within normal ranges.  Even with modern SIBO (small intestine bacterial overgrowth) testing, many breath and stool tests come back negative. Small intestine fungal overgrowth is often more common than SIBO, but it continues to go undiagnosed.

Even worse, you may have a positive breath test result multiple times (expensive) and still you haven’t seen any significant change in your symptoms or lab results. Either my patients (and myself) are crazy and there is nothing wrong with our digestion or there is something lingering that it slipping by traditional lab testing. SIFO or small intestine fungal overgrowth is one of the major findings in my office that many labs and patients are missing.

Underdiagnosed Imbalances Like SIFO

Studies done on patients with IBS have shown that over 60% of patients had some sort of infection in the small intestine, but when patients go to a traditional medicine doctor, rarely are these infections teased out.

In one recent study it showed that 40% of IBS patients had fungal overgrowth in their small intestine.  As far as I know, traditional medicine is not giving anti-fungal prescriptions for the digestive tract yet, very often at least. (I am not recommending a prescription anti-fungal.)

While I have many patients entering the office wanting me to determine if they have SIBO, I have yet had one ask if the have small intestine fungal overgrowth.  Looking at those above percentages, which don’t include the large intestine, sinuses, lungs and/or urinary tract, it is more common than not that someone who experiences digestive disturbances has an underlying infection of some kind.

SIBO (small intestine bacterial overgrowth) vs. SIFO (small intestine fungal overgrowth)

SIBO and SIFO can both cause digestive disturbances of almost any kind, but there is one distinguishing factor that makes me think its more of a fungal problem than bacterial and that is BLOATING!

Bloating, belching, gas and distention are clinical keys to knowing that you may have a fungal infection vs. a bacterial infection.  If you have gone on a low-carb diet and saw significant changes and then reintroduced carbohydrates only to have bloating or gas, you likely still have a fungal infection. The most common way women describe this is they say that by the end of the day they look “6 months pregnant”. 

Clinically I have noted that fungal infections also seem to elicit additional symptoms such as brain fog and fatigue more often than bacterial infections which seem to be more local in symptomatology. Another unique symptom often seen in the office that is associated more with SIFO than SIBO is a correlation to the ears.  I have found that small intestine fungal overgrowth often is correlated with excess ear wax, balance disturbances and having the feeling of “plugged” ears all the time.

And of course last, but not least, SIFO presents frequently with an itchy scalp, dry scalp, build up and/or dandruff. 

Because lab testing is still at its infancy for almost all chronic diseases; symptoms, a thorough patient history and a well-educated doctor is truly the best way to diagnose and eliminate SIFO. (Yes there are lab tests for small intestine fungal overgrowth, but they are either invasive or inconclusive.)

While it can be difficult to differentiate between SIBO and SIFO, sometimes you don’t have to.  Many patients can be found to have both at the same time and most of the herbs that I choose to use in my office will treat both simultaneously.

Other Infections (Small Intestine Viral Infection and Small Intestine Parasitic Infection)

SIBO is a relatively newly popularized diagnosis and now SIFO is becoming more prevalent in the functional medicine and natural medicine world, but we are still forgetting a few major groups of microbes.  Just like SIBO and SIFO existed before any lab test existed, so does SIVO (small intestine viral overgrowth) and SIPO (small intestine parasitic overgrowth). In fact if you are someone that has had chronic digestive issues it is most likely that you have 2 or more of these underlying imbalances disturbing your gut lining. 

Small Intestine Viral Overgrowth (aka SIVO)

Sometimes it can be hard to tell which infection you have on your own, but I have found the SIVO is more likely to cause food sensitivities. Or in other words, if you are person that can eat less and less foods each day, you may have a viral infection in your digestive tract. Small Intestine Viral Overgrowth usually presents with less pain and discomfort between meals and more upset right when they consume foods. 

Small Intestine Parasitic Overgrowth (aka SIPO)

Small Intestine Parasites often have the unique factor that they create severe stabbing pains or vomiting. They are also very unique in that they can be cyclical. For example, maybe you feel fine during the day, but at night you always have digestive pain. Or maybe your digestion acts up every weekend, but never during the week. (Assuming you have ruled out your excessive junk food and/or alcohol intake on the weekend.)

Without using all the fancy acronyms, and to simplify this lesson, essentially all I am saying is that there can be an imbalance of any organism in the small intestine. 

Natural Treatments for SIFO

If you have read my free eBook (If not, get it here.) then you know that one of the things that I feel makes my success rate in my practice so high is that I never compromise on using high quality products, specifically herbal anti-fungals.  The most common supplement I use to treat difficult SIFO problems is Chinese Coptis by AMG Naturals. If you have tried Coptis before and it didn’t help, then I recommend doing a combination of Morinda Citrifolia with Cistus Inancus to get to the more difficult fungi that are resistant.

While Chinese Coptis, Cistus Inanus and Morinda Citrifolia are the most common supplements that I use, I carry over 30 individual herbal antimicrobials that can effectively eliminate fungal overgrowth. Often times stacking them together at the same time is necessary.

If you have suffered from chronic candida infections for a long time and tried multiple rounds of antibiotics, then often adding biotin (B7) to your Cistus Inancus and Chinese Coptis can help significantly.

The second most important key to eliminating SIFO is to decrease your carbohydrate intake.  This includes all refined sugars, breads and starches.  Natural sweeteners like honey, stevia and maple syrup are best limited also, but can be tolerated in certain patients.  Essentially the goal of going low-carb is to avoid feeding the fungus while you are trying to kill it.

You shouldn’t have to be low-carb forever, but combining low-carb eating with herbal antimicrobials is the fastest was to see improvements. In general, some patients can tolerate more carbohydrates than others as a long-term dietary pattern, but to start you must decrease your carbohydrates significantly while using an herbal antimicrobial.

COMMON MISTAKE: Not treating everything at once.  Maybe you have decreased your carbohydrates before or been on an anti-fungal diet and maybe you have take herbs to treat SIFO previously, but adding the potent antimicrobial herbs at the same time as going low-carb is the key. I cannot tell you how many patients come in reporting that they have “tried everything” but because they were doing things one at a time or using the wrong supplements for small intestine fungal overgrowth (like probiotics, oregano oil, etc.) they didn’t get successful results and still battle symptoms.

Other Small Intestine Problems

While the small intestine in and of itself is important, maybe even more important is that it acts as a mixer of chemicals.  These chemicals (aka enzymes) are released from the liver, gallbladder, pancreas and stomach.  In order for the small intestine to be pain free and thrive, each of its cooperative organs must be assessed also.

Food sensitivities and intolerances are also common causes of small intestine bloating and pain. Histamine and inflammation of the small intestine are one of the reasons many people react to so many foods.  Caffeine, alcohol and certain spices can also irritate the small intestine during digestion.

Surprisingly enough, supplements can also be an irritant to the small intestine.  Are you one of those people that takes over 20 different supplements per day? Its most likely that one of those products is doing your gut harm. Probiotics can often irritate the small intestine if its not the right probiotic strain that you need. In my office I have patients come off of all probiotics while we do the low-carb anti-fungal diet combined with the herbal antimicrobials. Lectins are a hot topic right now and can irritate a sensitive small intestine, though I’ve never had to take someone off of lectins permanently.

If you are someone with recurrent or chronic fungal infections or candida, exercise can be a contributor to this pattern. For certain individuals that only train high intensity and don’t have an aerobic base (refer to Maffetone 180) you can perpetuate your own fungal dysbiosis by training your body to burn more sugar than fat. Your aerobic or anaerobic training affects the microbes in your body and can alter their expression. That being said, I recommend that patients and people in general make sure that they are mixing in long walks and slow training into their recovery protocols.


Small intestine fungal overgrowth is more common than most people think and while lab testing isn’t perfect, a thorough symptom survey and evaluation from a clinical expert can often get you started in the right direction.  Going low-carb and using the right herbal antimicrobial is the most common approach that give me my best results.  If you have tried those before, there may be more to your small intestine symptoms than simply a fungal infection.


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Dr. Houston Anderson is a top rated functional medicine doctor with expertise in natural treatments for IBS, leaky gut, SIBO, natural hormone balancing, food allergy and food sensitivity testing. He is a board certified Chiropractic Physician with a master's degree in Nutrition and Human Performance. He provides personalized natural medicine solutions to patients across the world.


  • Kenny

    Hey there

    Amongst the many countless pages I’ve come across regarding gastrointestinal woes concerning bacteria or fungus, yours seemed to have more detail in association with other problems in having (IE ear problems, constant brain fog , among others)

    I’ve been having some terrible issues with my stomach for the passed six years…that’ve gotten steadily worse to the pint where I’m constantly in pain and locked to the toilet for several hours back and forth in the morning. I can’t take long trips without randomly getting terrible stomach pains and needing to use the bathroom…discharge matter what I eat or if I don’t eat at all (which I usually don’t because I feel so yucky.) the type of pain I have varies, though it’s usually always on the right just above or below my navel…lately though, and I can’t figure out why the pains been at my left rig cage in the morning before moving back to the right and getting steadily more unbearable throughout the day. This problems pretty much taken over my life and I’ve tried so many things, antimicrobials (everything but what’s listed on this page, never heard of those until now!) probiotics, kombucha, yogurts, avoiding gluten, dairy…I may get minimal relief but only for a day or two then it’s back to misery. The brain frog is awful and the depression about it is crippling, if the pain doesn’t keep me in bed for hours anyways.

    I actually just moved to Arizona, I’ve seen a naturopath once before after saving up and she seemed knowledgeable enough, suggesting certain probiotics and other supplements,but she never did any follow ups with me, even after I did everything she requested including a mountain of paper work I sent her…that was a few years ago.

    I’m hoping functional medicine can still help because there’s days it just gets so bad I feel I’ll be stuck this way the rest of my life. Rarely have I read about anyone who’s really cured this or even gotten it enough under control to at least have a decent life. I’m hoping after I get settled maybe I can look into your offices, but until then I just wanted to let you know I really liked your page, I hope there’s something that can help


  • Kenny, you are not alone. Many of us have suffered with severe gut disorders in the past and many people overcome them. Functional medicine for IBS can definitely help, but most of the probiotics, etc. are just not strong enough to make much of an impact. Welcome to AZ!

  • EB

    All these are No-No’s for Sibo, & probably for other gut issues as well: Probiotics & Yogurt & Kombucha (one summit speaker said it’s basically alcohol, which is really bad for leaky gut, etc…) from all I learned on all the gut summits, until* a certain point in the healing…I’m no expert, but have gained an understanding of why these items have bothered us in the past.

  • EB, I don’t know what you are referring to as far as No-No’s. I do not suggest probiotics, yogurt or kombucha.

  • Michele

    Hello (again), I have three questions: I am currently taking (as of 8 days ago) oregano oil, Neem, cinnamon and Chinese coptis. Today is day 14 of the Elemental Diet, so I am slowly going to wean – but I also added Morinda and biotin today along with some well-boiled organic carrots (which sadly brought back all of the stomach gurgling I was trying to cure…or was it the Morinda???)
    Question 1: is it ok to be taking all of these at once? I am taking the recommended dose on the bottles, 3 times daily
    Question 2: I have purchased BFB-1 and BFB-2, as per your website and article on biofilm busters, but I have no idea what to do with them – I thought there were instructions on the bottles, but there are not.
    Question 3: I would like to consult with you, but I could not tell if you offer telephone consultations without an in person visit (I am in Maine). I will be in Sedona in September, so I can meet then, but September is a long time from now…..
    If you are willing to discuss my case by phone, what is the charge and how long is the appointment?
    Thank you again for your detailed and super-informative articles for those of us who have not had success with doctors (2 naturopaths who meant well).

  • Michele, I obviously cannot give specific advise for individuals on a website. The answers to your scheduling questions can be found here…

  • Jason X

    Is candida antibody panel (iga,igg,igi) useful in diagnosis of SIFO?

  • It can be helpful, but remember that the mycobiome is complex and candida ablicans is only one organism in a single species. So the most common finding is what is called a “false negative”. Meaning it shows up as negative, but it is still there.

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