Small Intestine Bacterial Overgrowth

Last April Dr. Allison Siebecker of spoke to our local GIG (Gluten Intolerance Group) chapter, and I planned to write it up that week. Here we are, nearly a year later, and I still haven’t done it!

A New IBS Solution

A New IBS Solution

At the time of the talk, I’d already been aware of SIBO (Small Intestine Bacterial Overgrowth) for quite a while. But sometimes you hear about a thing and just aren’t quite ready to deal with it. While she was talking, it all clicked into place.

Listening to Dr. Siebecker describe her personal battle with SIBO, I became near-certain that SIBO could explain the symptoms I’d had for so long and the reasons why I did well on GAPS intro but not so well when I started introducing many of the allowed foods.

But I didn’t get tested right away. Part of me didn’t want to go chasing after yet another thing that might be wrong with me. I didn’t want another test to come back negative, another battle with my negative self-talk that I’m a hypochondriac. The other part of me was afraid a test would show I had it and of what that would mean for the rest of my life.

Even now, here I am, getting distracted by facebook, emails, and what I’ve got in the oven rather than writing this post.

I knew I needed the test before deciding which treatment options to explore. But I waited 6 months untill I had insurance. Then I waited to make an appointment with my doctor. Then I waited to find a good time to go to the lab… and then for a good day to fast & prepare for the test. Finally I did the test, but didn’t get the results. There were problems with the lab not being able to fax my doctor. Eventually, nearly 3 months after doing the test and nearly a year since decided I needed to do it, I marched into the lab and got my results.

They indicated SIBO.

What is Small Intestine Bacterial Overgrowth?

By now you know all about how important it is to have a healthy balance of gut flora. But what you may not know is that all that life needs to be in the right place! It’s not enough to have good bacteria thriving in there… it needs to be where it belongs, and your small intestine is not it.

Several underlying problems work together or alone to create the conditions for SIBO.

A major cause of problems, the Migrating Motor Complex that naturally flushes bacteria and debris out of your small intestine isn’t working properly. Instead of getting moved on through, colonies of bacteria grow and thrive. When certain foods enter the small intestine, the bacteria have something to feed on. In the process, they release toxins and gasses. Depending on what kinds of bacteria are happiest, different gasses and toxins will be produced.

In a healthy person, this process happens between 90 to 120 minutes after fasting and about 9 times per day. Anything that slows or prevents this movement can predispose a person to SIBO. So people who are always snacking or eating small meals every two hours may inadvertently be shutting down some of the normal process that should be taking place, which could lead to overgrowth. However, they’d still have it functioning when they sleep. But for some of us, it gets shut down completely by nerve damage, other diseases, illness, medications, stress, and another causes.

Issues with the ileocecal valve also can lead to SIBO. This valve is a one way gateway between the small and large intestines. However, if it gets stuck open that gives a chance for material and bacteria from the large intestine to end up in the small intestine. When this backflow occurs and the Migrating Motor Complex is not doing its job, SIBO can occur.

Symptoms of SIBO

Most people with SIBO experience diarrhea, but those with the methane producing bacteria tend toward constipation. Some people get both! Most people get bloating, which is especially painful since it occurs in the small intestine which does not stretch as easily as the large intestine. Unpredictable stools, mucous in the stool, urgency, abdominal pain, and more are all common symptoms. Basically, what people have been calling IBS (Irritable Bowel Syndrome) is actually caused by SIBO in many cases.



But IBS isn’t the only symptom. SIBO can lead to a “leaky gut” which opens people up to a whole new range of symptoms. Molecules of foods can make it past the small intestine walls, triggering immune responses that causes new food allergies. Gluteomorphins and casomorphins can pass into the blood stream and across the blood brain barrier, causing mental health issues.

Malabsorption occurs when the gut lining is damaged, resulting in deficiencies and related problems like anemia and restless leg syndrome. Some types of microbes can metabolize bile salts, preventing the digestion of fats. Bad breath can be caused when gasses get into the blood stream and are then processed and exhaled by the lungs. Fatigue, fibromyalgia, worsened allergies, and all manner of systemic problems can be made worse or even caused by SIBO!

A few of the red flags that can point to SIBO include unexplained anemia (low ferritin), constipation that gets worse with fiber in the diet, and celiac patients that don’t feel better (or even get worse) even though they are 100% gluten-free. UPDATE: A study showed a higher correlation between SIBO and Fibromyalgia than SIBO and IBS! And the higher the hydrogen level, the higher the pain.

Testing for SIBO

Fortunately, testing for SIBO is usually non-invasive. However, it does require some preparation. Since the gasses produced by the bacterial overgrowths are exhaled, a simple breath test can provide answers. The patient prepares for the test by only eating very simple foods – plain broth and plain meat for at least one day, then fasting completely for another 12 hours prior to the test. No fiber or sugars should be consumed, because if the body is still working on processing those foods at the time of the test, the baseline values will be off.

Then you drink a sugar solution. There are two main versions of this test available: lactulose and glucose. Depending on the type of bacteria present and the location, different versions of the test will provide more accurate answers. A series of breath samples are collected, every 20 minutes for at least 3 hours. This is accomplished by blowing into a special collection tube. The lab then analyzes the samples for the hydrogen and methane levels. If the pattern of peaks of gas production and the amounts of gas production are too high, it indicates SIBO.

There is also another way to test for SIBO. A sample of digestive fluid is collected and cultured. This requires an upper endoscopy. Depending on your situation, if you are having this test done, it may make sense to also have biopsies collected in order to screen for celiac disease at the same time, even if your blood work for celiac was negative.

While some people assume that a culture of these fluids would be more accurate, that’s not necessarily the case for several reasons:

  • The fluid can only be collected from the first two feet of the small intestine. If the overgrowth is located closer to the ileocecal valve, the sample may not reflect the overgrowth.
  • The sample may be contaminated by saliva during the procedure.
  • We are not able to culture many of the strains of bacteria which thrive in the small intestine.
  • The small intestine is an anaerobic environment, a difficult condition to recreate during an endoscopy and subsequent lab work. Many of the bacteria will be killed rather than cultured.

Treatment for SIBO

Breaking the Vicious Cycle

There are several aspects to treating SIBO: Migrating Motor Complex stimulators (pro-kinetics), antibiotics, herbs, probiotics, and diet. Some people choose just one approach, while others use all of them. Here is a brief idea of how each contributes to managing SIBO.

I hope it’s obvious that you should not make your treatment decisions based on a website, especially one written by someone who is not a health care practitioner (like this one). I have not included all the details I have learned about treatment for that reason. You should consult with your doctor in person!


Because the bacteria in our guts feed on the food we eat, it’s important not to give them too much to chew on. The foods these microbes and bacteria like best are sugars. By eating a diet that does not contain foods that are appealing to the bacterial overgrowths, you starve them out.

The recommended diets for SIBO include SCD (Specific Carbohydrate Diet), GAPS (Gut and Psychology Syndrome Diet), Low FODMAPS (Fermentable, Oligo-, Di-, Mono-saccharides and Polyols), C-SD (Cedars-Sinai Diet – for maintenance only).

Many people are finding that a combination of GAPS/SCD and FODMAPS is more effective than either of those diets on their own.

In order to get a good clean start, the strictest version of the diet is followed when treatment begins. Then, more flexibility and more foods can be reintroduced. However, SIBO is not a disease that is usually completely cured, rather it is managed. As long as the underlying conditions that caused SIBO in the first place persist… ileocecal valve issues, stopped or slowed MMC, an unhealthy gut flora “fingerprint,” you will always be prone to it and may need to retreat periodically.

While some people who do diets like GAPS and low FODMAPS see them as a temporary diet that leads to healing. For people with SIBO, the diet may become less strict, but it generally amounts to a long-term life-style change.

Elemental Diet, Herbs & Antibiotics

An Elemental Diet (the studied brand is Vivonex Plus) can be used, but it is not a long-range treatment. It is used as a replacement for food for 2-3 weeks to give you a clean slate, much the way antibiotics would. The Elemental Diet is a liquid made up of amino acids, fats, and carbohydrates which are partially digested. It tastes disgusting and is made of nasty processed stuff, but it does work.

Therapeutic doses of antibacterial herbs can kill off the overgrowth. These are prescribed in concentrated doses for a period of time. The ones I’ve heard the most about include peppermint, oregano, garlic, cinnamon, and berberine herbs.

It’s important to note that just because they are herbs, they are not without side effects. These herbs are used as medicine, and they kill off the bacteria and are not necessarily any safer for you to use than other drugs, depending on your overall health status.

Rifaximin is the main antibiotic used in treating SIBO. It is non-absorbable and stays in the intestines, and actually had fewer side effects than a placebo when tested! This is an off-label use for the drug. It’s normally used for traveler’s diarrhea in much lower doses. For SIBO, there is a 10-14 day course involving very high doses. Because of the high doses needed and the less-known use of this drug, it may be difficult to get your health insurance to pay for it. Some doctors are finding that they can get it covered if they write a letter explaining the reason for the high dose.

Neomycin is also used, and it also has a local effect but has more chance of side effects. Another drug that may be prescribed along with the Rifaximin is Metronidazole, which does have systemic effects.

For the antibiotic treatments to do their best work, the bacteria does need to be actively replicating.




Many people who have embarked on a healing diet without understanding SIBO have been shocked to find that probiotics make them feel worse. Usually this is because the probiotics they chose to take included PREbiotics. Prebiotics are the fiber that the bacteria feed on. Adding bacteria food to a gut with bacterial overgrowths going on is a recipe for misery.

It turns out that probiotics do tend to help people who have SIBO, though. It’s just a matter of finding the right ones. If taking supplements, stay away from ones with fillers & prebiotics. If you are getting your probiotics from foods, make sure that they are completely fermented.

Migrating Motor Complex Stimulators

Some of the things that can help stimulate the Migrating Motor Complex Phase III contractions which are lacking in SIBO include:

  • Reduce stress – being in “fight or flight” mode temporarily turns off the MMC
  • Don’t snack between meals.
  • Get your rest.
  • Acupuncture for the MMC, ideally daily
  • Prokinetic drugs such as low doses of erythromycin

Recommended Reading

If you are interested in reading more check out the following books:

There is an explosion of research going on in this field. A huge amount is still unknown, there are many questions to be answered. What’s interesting to me is that so many people have independently come to the same basic idea of going on in our guts and have developed similar approaches to treating it.

Dr. Allison Siebecker, Dr. Mark Pimentel, Dr. Leonard Weinstock and others are leading the field. Google and search Youtube for their names to find out more as they share the latest about what they know with all of us!

Related posts:

7 comments to Small Intestine Bacterial Overgrowth

  • Great article, as usual! Thank you so much for sharing your experience with us–lot of useful information here.

  • Thank you for sharing this, I shared on Facebook too. I hope you will let us know what you end up doing for treatment.

  • Diane

    You blog was informational. I have been on a whole grain, fresh/frozen veggie, fruit and meat diet. I have lost about 45lbs. I would like to gain at least 10lbs back. I go back to the doctor next week. I’m hoping my bacteria levels have decreased, especially since I have basically starved for my health. I love to eat and the things I love to eat I cannot eat anymore. I guess I just want to gain some weight back. Thanks again, this really helped

  • […] finally went and got my SIBO test, with positive results! Finally, a real diagnosis explaining what was wrong with my […]

  • […] This study gives us a lot of good stuff to think about! So many people go gluten-free and still have digestive problems. That is even true for many people with celiac disease! There is a simple breath test which you can take that will measure your response to FODMAPs. (It is the same test that is used to diagnose SIBO.) […]

  • Thank you. Due to blood sugar issues, I have some trouble fasting/not snacking between meals. Would steamed low-fiber veggies and coconut oil be an acceptable snakc without impeding the MMC function too much?

    • I can not give medical advice and of course don’t know how important it is for you to continue eating between meals. I do think that snack would be preferable to most things I can think of, but I don’t know for sure whether it will impede MMC function. My interpretation of what I have read is that any digestion in process does impede it. But I have not seen studies about the various types of things you could eat and how they specifically affect it. My personal experience has been that the better my gut is in balance and the more I stay away from sweets in general, the longer I can go between meals without blood sugar issues. Having longer periods of rest for the digestive system is important for the MMC. But of course keeping your blood sugar stable is also important. I would work with a practitioner who can examine you in person, help you monitor your sugars, and knows about SIBO on this one.

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