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SIBO or small intestine bacterial overgrowth is a common problem I see on a day to day basis. SIBO affects a large number of people especially those with Celiac, IBS, or other gut related issues. It can often be difficult to treat and some patients feel better only to seemingly relapse shortly thereafter. In this article, I not only want to address SIBO but also its cousin SIFO. SIFO is small intestine fungal overgrowth. Both of these can cause a wide range of symptoms, so let’s get into it.

Small Intestine

The small intestine is the longest part of our digestive tract. Most of our nutrient absorption happens here. After food passes through the stomach crucial enzymes are added to aid in digesting. Food is broken down into smaller and smaller parts until we are able to absorb them.

The surface area of the small intestine is enormous too. It is not just a tube but has tiny hair-like projections throughout. When completely spread out, the small intestine would cover the size of two tennis courts!

It also contains a significant portion of our immune system. Many immune cells congregate here to fight infections and evaluate the happenings inside the small intestine. Which makes sense. What we ingest are still external to us until we absorb them. There are also beneficial bacteria present here, but not as many as the large intestine. These bacteria also protect us against pathogens. They help with absorption and can produce several nutrients for us too.

What is SIBO and SIFO?

SIBO and SIFO are characterized by the overgrowth of bacteria or fungus most often from the large intestine. It is often not a single one either, but several that overgrow. As I often say, most issues are multifaceted.

Both of these can significantly interfere with digestion and absorption. They can damage the cells of the small intestine leading to leaky gut, which I have talked about elsewhere. Leaky gut is leaked to many different issues including autoimmunity.

What causes SIBO and SIFO?

There are several factors involved. Diet is a big component but so is the overall stress load on the body. Stress affects the body in many ways but a common one is decreasing stomach acid production. But that is just one factor.

Other factors include dysfunctional ileocecal valve which lies between the small and large intestines, food intolerances, antibiotics, diabetes, and many other issues. If you would like to learn more here is a study that covers it in even more depth.


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One of the main symptoms is bloating and discomfort. It can be quite painful. I have had it myself. Definitely not enjoyable. Many complain of either diarrhea or constipation. Flatulence and belching are also common.

The abdomen can be quite distended with the amount of gas. I have also noticed eating certain foods can exacerbate this quite a bit. Sometimes I and others have recommended a FODMAPs diet to reduce the fermentation of certain carbohydrates. This can significantly help the bloating but is not a long term solution. Though diet in general is still very important.


Most functional medicine doctors will order a SIBO breath test to diagnose it. It is important to note that this is so far the best way, but can still miss it at times. It is also important to note that SIFO does not have a reliable test.

Therefore a thorough history is important. My patients sometimes complain about the length of my intake forms. But it is important to get a full health history to determine what is going on. This coupled with appropriate tests helps tremendously in the process.

Natural Approach

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So how do we approach this naturally? First of all diet. The standard American diet is pretty atrocious. It is filled with refined carbs, processed foods, and completely out of balance with our biology. Humans evolved on a specific set of foods. It doesn’t mean there is one way of eating. One thing anthropology has showed us is that humans are very capable. All around the world people eat a variety of foods and thrive. That being said we can learn a lot from our hunter-gatherer ancestors. There are certain principles that are timeless.

Diet alone is not going to do it for most people though. It is important to get a full functional medicine work up. This includes appropriate blood work and testing. In the office, I go a step further and test with applied kinesiology. It helps fine tune the process, it is not necessarily diagnostic but nonetheless a very helpful tool. It is how I found out I was gluten intolerant. Not believing it at first, I tried it for 3 weeks and noticed a remarkable difference. I went from having daily migraines to none. I mean none. Time and time again AK has proved its usefulness as a neurologic test. After hitting diet, I will touch on the other crucial elements.


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I start people off with a paleo template which is nutrient dense and excludes many foods that are inflammatory such as grains, sugar, and for some dairy. I think dairy is a perfectly healthy food if it is tolerated. Paleo is great starting point. Then I look for food intolerances which could be gluten, corn, dairy, soy, nightshades, or others. These will be the highest priority and removing them from the diet will be a must. Depending on the client I may need to tailor things in a step-by-step process because the change can be very hard.

An important element of diet that I emphasize is the significance of animal foods. Our ancestors ate a lot of animal-based foods particularly prizing organs. Why? They are by far the most nutrient dense foods on the planet. In order to heal and maintain good health the body needs many nutrients such as vitamins A, C, E, and B12. There are many others such as essential amino and fatty acids. Animals pack the most nutrients. So balancing the diet will allow for the greatest abundance of nutrients while minimizing inflammatory foods especially those that can spur further issues with SIBO via fermentation. Onion and garlic are two common ones.

SIFO requires some additional requirements as do all fungal infections. I put my clients on an antifungal diet. This excludes sweeteners of every kind including dried fruit and fruit juice. It also removes any foods fermented from mold such as alcohol, kombucha, soy sauce, or cheese.

Another component to check is the oxalate toxicity and mold exposure. Prolonged fungal infections can be connected with oxalates. Fungi can produce oxalates and an overload of oxalates in the diet should be evaluated in difficult to treat fungal issues. Mold in the home or at work can also exacerbate or prolong the treatment process. Mold toxicity is common and can be quite terrible. So with fungal issues, mold exposure should be considered in the treatment process.

Other Crucial Elements

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As I said, diet is often not enough. So it is important to be evaluated for appropriate aids. Herbs are a great tool to support the body’s natural healing processes. Many herbs have antifungal and antibacterial properties which can greatly help in SIBO and SIFO cases. They also have other properties which can assist in detoxification of microbial toxins and other toxic exposures. Pesticides and heavy metals being some of the most common.

It is important to address all stressors whether related or not. These can greatly affect the body’s ability to heal and can contribute to things like leaky gut. Glyphosate is well known to cause leaky gut and dysbiosis issues. That is why I emphasize organic so much. General stress from daily life also needs to be considered as emotional stress from work and relationships can dampen the body’s ability to heal as well.

Lastly, supplements such as molybdenum, zinc, vitamin A, and others may be needed. Molybdenum helps with the detoxification of aldehydes that fungi can create. Zinc is needed in many processes including the immune system. Vitamin A is as well and it is very helpful in healing the gut. Glutamine is a common amino acid used to help leaky gut, but the underlying cause should be addressed otherwise some supplementation is like pouring water into a leaky barrel. Nevertheless, they can be helpful in the meantime.


Hopefully this gives you a broadview of SIBO and SIFO, and maybe some helpful tools in approaching it. You can definitely try an animal-based paleo diet but the likelihood is you will need to get evaluated. Definitely look for a functional medicine doctor in your area, most are quite skilled in addressing these issues or at least can point you in the right direction.

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