What is SIBO? Causes, Symptoms & Treatments

What is SIBO?

Digestive problems such as abdominal pain/discomfort, diarrhea, constipation, bloating, and/or reflux are a common complaint among patients with chronic health issues.   Many of them have been given the diagnosis of Irritable Bowel Syndrome (IBS), which was once thought to be a diagnosis of exclusion.  In other words, after ruling everything else out it was, and still is, common for a physician to say that you must have IBS.  But, what is IBS anyway and do we know what causes it?  According to Dr. Pimentel(1), in the last decade, we have discovered that IBS is no longer a syndrome, but a disease, and there are known causes.  One of these causes is a condition called Small Intestinal Bacterial Overgrowth or SIBO.  It is this condition that is now becoming more recognized in the functional and traditional medicine communities.

Most IBS is caused by SIBO, which is identified by a breath test and then treated.  SIBO occurs when there is an overgrowth of bacteria in the small intestine.  SIBO is not a diagnosis, but a condition caused by something else that results in the slowing down of the normal digestion process.  Slow digestion causes bacteria, which should normally reside in the large intestine to “back up” and end up in the small intestine where they shouldn’t be. The small intestine should be relatively clean.  There are greater than 1 trillion bacteria/nl in the colon compared to the small intestine where there should be less than 1,000 bacteria/nl (1).   When this happens, patients may experience symptoms of IBS: diarrhea, constipation, or a combination of both types.  According to Dr. Pimentel, a world leader in the diagnosis and treatment of SIBO, not all IBS is caused by SIBO but a large majority is.  “SIBO causes 60% of IBS of the diarrhea and mixed type and 80% of IBS of the constipated type” (1).


The problem with this is that the overgrown bacteria start to interfere with both the structure and the function of the small intestine.  This means that we will not digest or absorb important nutrients of our food.  The over-grown bacteria damage the gut lining causing “leaky gut” or intestinal permeability.   You may have a pristine diet, but still not be absorbing all the important nutrients you need because the gut wall is compromised.  This may also cause a problem with fat absorption resulting in fatty stool and deficiencies in Vitamins A and D as well as an increase in food sensitivities.   Symptomatically one may feel pain, nausea, gassy, bloated, or experience diarrhea and/or constipation.  These bacteria also excrete enzymes, which have been shown to produce cognitive and neurological symptoms like mood disorders, depression, ADHD, and autism (3).

What causes SIBO?

The problems associated with SIBO occur when something causes the migrating motor complex, (MMC) or the small intestine’s “cleaning action wave” to slow down.  “Patients with SIBO have significant delays in small bowel transit time as compared to those who don’t (4).” In an uncompromised person, the MMC sweeps the small intestine clean between meals and during the night.   When this does not work well, like a river that stops flowing, stagnation occurs in the small intestine causing bacteria to grow and multiply.  Some common causes of this reduced cleaning action wave are: Celiac, Crohns, Lyme, pain medications, low stomach acid, Proton Pump Inhibitors (meds that reduce stomach acid), nerve damage in the gut lining from a bacteria (H. pylori or food poisoning), adhesions from surgery, moderate to heavy alcohol use, vagus nerve dysfunction, diabetes, reduced stomach acid, Diverticulitis, Scleroderma, adhesions from endometriosis, or missed appendicitis.  In a retrospective study done in 2014 that assessed ileocecal junction pressure (ICP) (the valve between the small and large intestine that helps keep bacteria out of the small intestine) intestinal pH and small bowel transit time (SBTT), it was found that in patients with SIBO, ICP was significantly lower, SBTT was slower, and pH was higher (5).   In other words, SIBO is associated with slow digestion, inadequate valve pressure between the large and small intestine, and decreased acidity, which allows bacteria to back up and overgrow in the small intestine.


Recently, there have been exciting new insights into the cause of IBS-D (diarrhea), particularly regarding the role of food poisoning and acute gastroenteritis and how this changes the gut bacteria.  Cytolethal distending toxin B (CdtB) is a toxin that is produced by the bacteria that cause food poisoning and acute gastroenteritis.  In a recent study looking at IBS-D in Inflammatory Bowel Disease and Celiac Disease subjects compared to non- IBS, healthy controls, two specific antibodies, anti-CdtB and vinculin, were both found to be elevated. These results confirm that anti-CdtB and anti-vinculin antibodies are elevated in IBS-D compared to non-IBS subjects(5).   So, the body creates an antibody to the CdtB toxin (from food poisoning), which looks similar to our own bodies protein molecule, vinculin.  The vinculin molecule helps the gut cells to communicate, contract, and provide the “cleaning action wave” that it needs to keep bacteria levels low.  Because of the similar structure of vinculin to CdtB, (which we call molecular mimicry) the body produces anti-vinculin antibodies.  This is an autoimmune reaction, when our own body attacks and damages the cells of the intestinal wall.  Food poisoning may affect the intestine’s function causing bacteria levels to go up and SIBO to develop.  This also suggests that we may be able to diagnose IBS-D by measuring the antibodies to CdtB and Vinculin (6).  The newest test available to diagnose this is called IBSchek, which measures the antibodies for both CdtB and vinculin and may be helpful in distinguishing between IBS and Inflammatory Bowel Disease (7).

What are the symptoms of SIBO?

The overgrowth of bacteria in the small intestine starts to ferment food here instead of the large intestine and produces an excessive quantity of hydrogen and/or methane gas.   These gases then cause the intestine to slow down further which may cause the following symptoms:

  • Abdominal pain and/or cramps

  • Abdominal bloating and distension

  • Belching and/or flatulence

  • Constipation and/or diarrhea

  • Nausea, heartburn, reflux

  • Skin issues- (rosacea, eczema)

  • Food sensitivities

  • Malnutrition (B12, D, iron deficiency)

  • Histamine intolerance

  • Water retention

SIBO testing

SIBO testing is recommended only after other testing has been completed to rule out a gastrointestinal issue such as an H. pylori infection, parasite, or fungal overgrowth.  There are two ways of testing for SIBO: endoscopy and hydrogen/methane breath test.  The issues with endoscopy are that it is invasive and expensive with limited scope of evaluation (only the first 6 inches of the small intestine can be tested).  Most of the bacteria causing dysfunction are located toward the end of the small intestine, closer to the large intestine.  More importantly, most anaerobic bacteria cannot be cultured.

As hydrogen and methane gases are only produced by bacteria, not human cells, the hydrogen/methane breath test is a more accurate way by which we can assess the presence of SIBO.  This involves ingesting a solution of lactulose, a synthetic sugar that can only be digested by bacteria.   The bacteria then give off one or both of these gases that we can then measure in the breath.   There is one additional gas, hydrogen sulfide, which cannot be measured directly at this time, although, according to Dr. Pimentel, there will be more data coming out about this gas in the next few months (1).  

The hydrogen/methane breath test is a three hour test with measurements taken every twenty minutes.  The two hour tests are not recommended as this may not provide enough time for the sugar solution to reach the lower part of the small intestine.  Prior to testing, there are some diet and medication restrictions.  This test is important to confirm the presence of SIBO as well as the type of gas to determine the best treatment program.   Once treatment has been completed, re-testing is necessary to determine the decline in gas levels and if continued treatment is required.

SIBO treatment

SIBO treatment has come a long way, but there are still issues with clinician experience and the treatment itself.  Previous treatments and some that are still used for SIBO include: anti-depressants, fiber, laxatives, and medications that stimulate the serotonin receptors in the gut to assist peristalsis or contraction of the intestinal wall, (like Resolor).  According to the consensus at the 2016 SIBO/ IBS Global Outreach Symposium, most practitioners are using a combination of antibiotics (Rifaximin), herbal antimicrobials, and diet; however, there is always the risk of antibiotic resistance even with the herbal antimicrobials.  Also, there are not many physicians who are even familiar with SIBO evaluation or treatment as it is a relative newcomer to the medical research scene since the mid to late 90’s.

An antibiotic treatment is generally a two week program compared to the herbal antimicrobials, which require about a thirty day program, depending on severity of symptoms.  In a multi-center study, including Johns Hopkins University, it was found that herbal therapies are as effective as antibiotics in the treatment of SIBO (8).

Probiotics are best avoided during treatment and at least for a few months after treatment.  Even though probiotics (and prebiotics) are good for gut health, in SIBO patients, they may feed the overgrown bacteria, so they are not recommended during the healing period.

Retesting is then important to evaluate how well the treatment worked, if gases have decreased, and if additional treatment is necessary.  Unfortunately, the recurrence rates are relatively high.  According to Dr. Pimentel, in patients with high hydrogen breath tests, recurrence of SIBO is 13% after 3 months, 28% after 6 months and 44% after 9 months(1).  This implies that repeat treatment will most likely be necessary in addition to specific diet restrictions.

After treatment and re-testing, a combination of the Specific Carbohydrate Diet (SCD) and the Low Fermentable, Oligosaccharide, Disaccharide, Monosaccharide and Polyol Diet (Low FODMAP) are recommended.  This combination diet has been developed by Dr. Alison Siebecker, a naturopathic physician who specializes in SIBO(9).  Others may add in the Fast Tract Diet by Norman Robillard, Ph.D, founder of Digestive Health Institute that emphasizes low fermentation foods(10).  In addition, patients should not snack between meals to allow time for the natural sweeping action of the intestines.

Once the bacteria killing phase is completed, most patients will require some type of prokinetic, a supplement or medication that assists the MMC to do its job.  The nerve cells lining the small intestine are often damaged from a bacteria (food poisoning) or diabetes, which will perpetuate the stagnation of food thus continuing the cycle of SIBO.  Types of medications may include low-dose Erythromycin, low-dose Naltrexone, or natural herbal therapies.

Other helpful treatments include the use of digestive enzymes including Betaine HCl to bring acidity up (as we know patients with SIBO have higher pH levels) and ox bile to encourage better breakdown of food, so it does not become food for bacteria.  If nerve damage is present, then therapies to strengthen the Vagus nerve are encouraged (like gargling or singing loudly) (11).

Finally, it is necessary to heal the gut lining from the damage caused by the bacterial over-growth and restore the gut microbiome.  This can be done with a combination of herbal therapies and a very gradual reintroduction to higher FODMAP foods as well as pre and probiotics.  

Until recently, the cause of IBS was unknown.  It was common for patients to receive an IBS diagnosis after everything else was ruled out. Now, we know that a significant amount is caused by a condition called SIBO.  SIBO from food poisoning causes the body to attack itself, which damages the cells lining the intestinal wall that help the intestines contract and move food through.  We can test for the antibodies that are produced during a food poisoning event, which may be helpful in determining if the patient has IBS or not.  We can determine if SIBO is present by doing a breath test, measuring gases, and treating with either antibiotics or antimicrobials.  As there is a relatively high level of recurrence, this particular condition involves careful attention to diet as well as prokinetics and therapies to keep the small intestines working well to minimize bacteria overgrowth.  It is encouraging that there is now more awareness and research on IBS and SIBO.  Hopefully, as more physicians and clinicians become educated in this disorder, there will be easier access to both evaluation and treatment with better outcomes.

  1. Pimentel, M. “IBS and SIBO.” Global Outreach Symposium of IBS and SIBO. Cedars-Sinai Medical Center, Los Angeles, CA. 5 Nov. 2016. Lecture.

  2. Gorbach, Sherwood L. Medical Microbiology.4’th edition. Galveston:Baron, 1996. Print

  3. Galland, L. (2014). The gut microbiome and the brain. J Med Food. Dec;17(12):1261-72. doi: 10.1089/jmf.2014.7000.

  4. Roland , B. C., Ciarleglio, M. M., Clarke JO, J. O., Semler, J. R., Tomakin, E., Mullin, G. E., & Pasricha, P. J. (2015). Small Intestinal Transit Time Is Delayed in Small Intestinal Bacterial Overgrowth. [Abstract]. J Clin Gastroenterol, Aug(49), 7th ser., 571-576. doi: 10.1097/MCG.0000000000000257.

  5. Roland, B. C., Ciarleglio, M. M., Clarke, J. O., Semler, J. R., Tomakin, E., Mullin, G. E., & Pasricha, P. J. (2014). Low Ileocecal Valve Pressure Is Significantly Associated with small intestinal bacterial overgrowth (SIBO). (Abstract) Dig Dis Sci., Jun;59(6):1269-77. doi: 10.1007/s10620-014-3166-7.

  6. Pimentel,M,, Morales, W., Rezaie, A., Marsh, E., Lembo, A., Mirocha, J., Leffler, D.A., Marsh, Z., Weitsman, S., Chua, K., Gillian, M., Bortey, E., Forbes, W., Yu, A., Chang, C., Development and Validation of a Biomarker for Diarrhea-Predominant Irritable Bowel Syndrome in Human Subjects. PLoS One. 2015 May 1; 10(5): e0126438

  7. http://www.healthywomen.org/content/article/new-test-gives-faster-diagnosis-ibs

  8. Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., . . . Mullin, G. E. (2014). Herbal Therapy Is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth. Global Advances in Health and Medicine, 3(3), 16-24. doi:10.7453/gahmj.2014.019

  9. http://www.siboinfo.com/diet.html

  10. https://digestivehealthinstitute.org/author/normjr1/

  11. Kharrazian, D. (2013). Why isn't my brain working?: a revolutionary understanding of brain decline and effective strategies to recover your brain's health. Carlsbad, CA: Elephant Press.

Anne Lemons