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SIBO: A good thing gone wrong

IBS is the most common GI disorder, affecting millions of people and contributing to 10%-ish or more of doctor’s visits in the U.S. Now, has anyone ever mentioned a potential root cause of your IBS?

Probably not, even though SIBO is now thought to make up for 50% or more of IBS cases. Unfortunately, many of you get the diagnosis of IBS and you’re sent on your way with no real resources to address the underlying issue.

What is 'SIBO'?

SIBO = "Small Intestine Bacterial Overgrowth"

SIBO is tricky because it’s not necessarily a bad invasive pathogen (although it can be), but is often a case of a good thing gone wrong. The small intestine is supposed to be sterile, meaning no bacteria should live there. And our body’s beneficial bacteria are supposed to live in the large intestine, where they fortify the gut with digestive power and form a protective barrier against toxins and pathogens (bad guys). However, in certain cases of imbalance, those good bacteria can migrate into the small intestine and wreak havoc on digestion, absorption, and overall balance in the body. There are even cases of SIBO contributing to infertility and rosacea. For anyone who’s dealt with SIBO, you know the bloating and discomfort can be fierce, and the ripple effect of SIBO throughout the body is even broader.

There are 3 types of SIBO:

Hydrogen, methane, or hydrogen sulfide dominant, which are named after the type of gas emitted by the specific bacterial inhabitants. There is even a (sort of) 4th type called SIFO, or small intestinal fungal overgrowth.

Symptoms of each subtype are slightly different, and therefore require different tools to resolve. Hydrogen-dominant SIBO is usually associated with diarrhea, and methane-dominant is more often associated with constipation. Hydrogen sulfide SIBO can produce alternating constipation and diarrhea, and often a strong sulfur-smelling stool or gas.

What Causes SIBO?

There are several known triggers of SIBO including food poisoning and chronic antibiotic use, but several more subtle risk factors include:

  • Low stomach acid (due to hypothyroid, acid-suppressing medications, or low B12)

  • Abdominal surgery

  • Chronic constipation

  • Low bile acid flow (sluggish liver/gallbladder)

  • Traumatic brain injury

  • Medications (acid suppressors, Accutane, antidepressants, opioids)

What are the Symptoms of SIBO?

Symptoms of SIBO can include:

  • Bloating (especially in the upper gastric area under the rib cage)

  • Abdominal distension (think looking and feeling 6 months pregnant)

  • Nausea/indigestion

  • Burping/Hiccups

  • Gas/intestinal cramping

  • Diarrhea

  • Constipation

  • Loss of appetite

What to do if you suspect you have SIBO

SIBO is sometimes tested and/or treated in a traditional GI doctor’s office, but there is often very little structure around the process and so the recurrence rate (meaning repeat infections) is more than 80%! That is a very disheartening statistic and part of why I’m so passionate about spreading the word about SIBO and general gut health! We can do better than this! No one should have to deal with repeated cycles of GI distress and discomfort, treated only with round after round of antibiotics which ironically make the gut weaker than before the infection!

From a functional nutritional standpoint, we have many more tools in our toolbox to not just manage, but resolve SIBO!


Breath Test

A hydrogen/methane breath test involves drinking a lactulose sugar solution and then breathing into a special bag over the course of 2-3 hours, which measures levels of gas produced by certain bacteria.

Stool Test

There are several vendors who offer comprehensive stool testing, which is more of an indirect method of assessing SIBO, but can still be useful and also provides a lot of other information about the gut including inflammatory markers, digestive insufficiency, and beneficial bacteria diversity.


When treating SIBO from the Functional Nutrition standpoint, there is a four-pronged approach including: diet, Herbal antimicrobials, Probiotics, & support products.


This is a management technique employed by many traditional dietitians. It works, and has significant research behind it, but is not a long-term solution. If someone tells you that’s the only way, RUN! Reducing fermentable carbohydrates are extremely helpful in managing symptoms, but long-term gut health thrives on these resistant starches and fibers, so ultimately the goal is to be able to kill the infection and then repair and feed the gut for long-term health and immunity.

I use the low FODMAP and SCD diets frequently in my practice to help clients manage bloating, constipation, and diarrhea. The low FODMAP diet limits fermentable carbohydrates which, in an irritated gut, can contribute to worsening symptoms. SCD is similar but also excludes all grains, not just wheat as is the case with low FODMAP. Sometimes a hybrid SCD/low FODMAP works well for severe cases to minimize restrictions and maximize food enjoyment. Every body is different, so I suggest working with a knowledgeable dietitian, especially if you have been on a restrictive diet for more than several months; or if you’ve tried one or the other and not had success.

Note: hydrogen sulfide SIBO does not always respond to a low FODMAP diet, and seems to be more associated with a sulfur intolerance. Therefore, the dietary approach for hydrogen sulfide SIBO is completely different than methane or hydrogen-dominant SIBO, and symptoms are usually best managed by temporarily limiting rich sulfur foods such as meat, eggs, onions, certain fruits, and cruciferous vegetables.

Herbal antimicrobials

Fortunately SIBO responds very well to herbal antimicrobials; some studies indicate they work equally or even better than prescription antibiotics! Some of my favorite antimicrobial herbs for SIBO include berberine, oregano, garlic, uva ursi, olive leaf, and neem. Now if you have to take an antibiotic, to make you feel better there are some studies which show that certain antibiotics like Rifaximin may actually reduce inflammation and support beneficial Bifido bacteria production. However, antibiotics can still reduce overall gut flora diversity, and I don’t prescribe anyway, so herbs are my go-to for natural, effective support.


Treatment of SIBO with probiotics is tricky, because often these same good bacteria are part of the problem merely because they are in the wrong place (small intestine vs large intestine). So introducing more bacteria, even if it’s beneficial, could “feed” the bacteria which have migrated into the small intestine, and essentially make symptoms worse.

There are, however, a few key strains of probiotics that can naturally support the immune system without adding fuel to the fire of bacterial overgrowth. Saccharomyces boulardii, a probiotic yeast, inhibits toxins, reduces diarrhea, and regulates the immune response. This is a helpful tool for SIFO as well as hydrogen-dominant SIBO, which is usually associated with loose stools. Some spore-based probiotics can also help regulate the immune response without aggravating bacterial overgrowth or worsening symptoms of bloating. I use these strains with methane-dominant SIBO and SIFO cases so that we can begin to rebuild immunity in the gut without aggravating the bacterial overgrowth. I don’t usually use probiotics with hydrogen-sulfide SIBO cases until the bacterial imbalance or dysbiosis is resolved.

Support products

Liver and digestive support are extremely important in treating SIBO. Depending on symptoms and stool test results I utilize various nutritional products for liver support and to improve motility and digestion. Beets, lemons, and cold-pressed flax oil support liver and gallbladder function. Digestive enzyme and motility agents like ginger and artichoke can be a huge help to keep bowels regular, especially with tough methane-dominant SIBO cases where constipation can be severe.

Closing remarks about SIBO + you...

SIBO is a tricky beast, so don’t go it alone! It is important to not only manage symptoms but to get to the root cause. And if there are additional health issues, there may be more work to do once SIBO is resolved in order to fully rebalance the body. If you’re experiencing symptoms of bloating and/or constipation or diarrhea, work with a knowledgeable dietitian or functional medicine provider to identify and resolve the condition. Don’t take a lazy diagnosis of IBS as a final answer-get to the root cause!

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