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  • Writer's pictureGavin Guard, Medical Director

Why is my digestion so messed up?

Updated: Jan 22, 2022

Key Takeaways

  • SIBO stands for “Small Intestinal Bacterial Overgrowth”

  • Up to 50% of those with Irritable Bowel Syndrome (IBS) have SIBO

  • SIBO describes the presence of too much or abnormal types of bacteria in the small intestine

  • Breath testing is a novel way to assess if you have SIBO or not

  • There remains no consensus of what counts as a SIBO diagnosis

  • Treatment with antimicrobials can be used with or without testing for SIBO


Are you suffering from chronic gut complaints like gas, bloating, diarrhea, and/or constipation? Or perhaps you realize that non-gut symptoms like joint pain, brain fog, rashes, and fatigue can be attributed to poor gut health?

If this is you, then tune in to the rest of this article. In this piece, we uncover a little-known diagnosis that often goes ignored in a conventional medical setting. We also review what some potential tests are and what to do about it. Enjoy!

What is SIBO?

It’s probably no surprise that our body hosts other microorganisms. The collection of 11 pounds of microorganisms is called the “microbiome” and it consists of all the bacteria, viruses, parasites, and amoebas that call our gut, skin, and mouth “home”. Normally, the small bowel houses a small number of bacteria whereas the large intestine contains the majority of our bacteria (5).

SIBO, IBS, Gavin Guard
IBS affects about 1 in 5 people

Within the last few decades, researchers have recognized that the small bowel can have an “overgrowth” of bacteria. This is correctly called Small Intestinal Bacterial Overgrowth or “SIBO” for short. It has been recognized to be a real condition as outlined by many medical organizations (13).

Furthermore, SIBO is present in around 30-50% of those with irritable bowel syndrome (diarrhea, constipation, abdominal discomfort, gas, and bloating). Perhaps not surprisingly, IBS has found to affect 1 out of 5 people (11).

It’s been documented that SIBO, or dysbiosis more broadly, is associated with conditions like IBS, IBD, liver disease, celiac disease, renal disease, and chronic pancreatitis (12). It’s also thought to cause deficiencies of carbohydrates, fat, vitamins B12, D, A, E as well as minerals such as iron and calcium (8). One paper found that SIBO was present in 93% of those with fibromyalgia (16).

Our clinic can help not only with your gut health but also what lead to poor gut health in the first place.

Testing options for SIBO

The conventional “gold standard” for SIBO testing is the aspiration and culture. This is where a GI doctor sticks a tube into your gut and samples the fluid in your small bowel. They then take this fluid sample and place it onto petri dishes to see how much grows. Papers disagree as to the exact amount, but bacterial counts higher than 105 on a small bowel culture remain a common cutoff by many researchers and clinicians. However, one study noted that this many bacteria have been found in healthy people without any gut symptoms who eat a lot of fiber (10).

I don’t see a lot of you signing up for that procedure. It’s limited by its high cost, practicality issues, and the fact that only 20-30% of bacteria can be cultured (9). Furthermore, one study found that in a group of 80 patients with IBS, 15 had SIBO when using culture but only 4 of these 15 participants were positive on a glucose breath test (4). This is a big discrepancy depending on the testing methodology.

The limitations of the culture have brought to the wide-spread use of breath testing. The theory is that specific type of bacteria (gram negative anaerobic bacteria) produce gases (hydrogen, methane, or hydrogen sulfide) when exposed to sugar like glucose or lactulose. A portion of these gases (about 20%) get absorbed into the bloodstream and through a process of diffusion, get exhaled by our lungs (5). We can measure these gases over a course of 2-3 hours at 20-minute intervals to assess for high levels of gases.

But is this a good test? Let’s find out.

SIBO breath test, Gavin Guard
example breath test of one of my "SIBO negative" patients

Is breath test a good test for SIBO?

Most studies have pointed to the association of IBS and SIBO. Using glucose, IBS patients were 2.6 times more likely to have SIBO than healthy controls (3). The prevalence of SIBO in those meeting criteria for IBS has been as varied as much as 4.3 to 83.7%. Why such the huge variability?

Most of this variability comes down to the flaws of SIBO breath testing.

The first problem arises with the problem with finding a good sugar (glucose or lactulose) to use. A big contention has arisen between whether we should use glucose or lactulose substrate. It looks like glucose may be a better sugar solution to use for the breath test (9,10,11).

With that said, even the better test (glucose) only picks up on SIBO just 50% of the time.

The second problem is that there is no agreed upon consensus on the gas cutoff points to where we say a patient does or does not have SIBO. Some say a hydrogen level >12 ppm is positive, whereas others say a level >20 ppm is positive. Perhaps a better approach would be to use clinical symptoms as a guide and treat with broad spectrum antimicrobials after first line therapies have been used without success.

Finally, is the problem of how to know if the sugar solution is in the small or large intestine when the gas levels rise. One study of 139 patients found that 48% of breath test results were falsely positive when researchers gave a radioactive labeled glucose solution. Most clinicians use a cutoff point of 90-minutes but one study found an average of 70-minutes as the time when the sugar solution reaches the large intestine. If a rise in gas was noted at 80 minutes for example, an over-zealous clinician may label someone as “SIBO positive” when it may in fact be a normal response.

One study found that a breath test may indicate an altered microbiome, rather than overt overgrowth (15). I think this is a better description of a “positive” breath test.

You can talk to your functional medicine clinician about getting a comprehensive assessment your gut health.

How to best assess and treat “SIBO”

Long-story short is that there remains no consensus on what SIBO actually is. We have theories but no good guidelines to go off of. I have used to move breath testing less in practice.

A good way of using it after looking at the research is to not necessarily see who has SIBO but rather to predict who would benefit from an antimicrobial approach like the use of a special antibiotic called Rifaximin, which is FDA-approved for those with diarrhea type IBS (12,14). However, clinical trials have used Rifaximin in those with IBS without the use of breath testing before-hand, which have showed a success rate of 40% of study participants (which is a pretty good response rate for a medication).

At the moment, we have more valid and well-founded tests like blood chemistry to assess the health of patients. I believe blood chemistry should be a top priority to help my patients understand their overall health patterns before moving towards more gut-specific tests such as a breath test.

With that said, a breath test often does not change management. Perhaps, it can tell us if hydrogen sulfide SIBO is present and necessitates a different treatment regimen. But I will often opt to perform an empiric rounds of antimicrobials and assess for symptom improvement. This saves my patients over $200 in most cases and would allow us not to become “SIBO-centered” in focus, but rather treat the person as a whole.

Considering that breath testing can be elevated when the patient feels “good” or vice versa, we should rather go off blood chemistry results and how the patient is actually feeling rather than multiple repeat rounds of testing and treatment. In fact, a meta-analysis of 10 studies suggested that the success rate of antibiotics is only about 51%.

In addition, 44-66%% of patients relapse with their symptoms by 9 months (1,12). This often leads to the need of multiple rounds of treatment. This poses a risk of antibiotic resistance and C. diff infection. Instead of another round of antimicrobials, maybe we should pause to ask why dysbiosis/infection is able to form in the first place.

One paper noted that “the causality of SIBO and IBS can’t be concluded from the case-control studies as such a design merely proves an association” (3). Maybe there’s something wrong with the immune system that is allowing for dysbiosis to occur. This is where we have to turn to the general health of the body and address things like food sensitivities, nutrient imbalance, psychosocial stressors, etc. We can also think about other interventions for gut health such as probiotics, fiber/prebiotics, elemental diet, prokinetics and further digestive support and replacement.

The Bottom Line

SIBO is a new and exciting diagnosis and is linked with other conditions like IBS, IBD, fatigue, and liver disease. With that excitement comes some uncertainty.

Right now, breath testing remains the most practical and cost-effective way of testing for SIBO. However, I think a better way of assessing and treating gut dysfunction is to get more validated tests like blood chemistry that gives an idea of overall health patterns.

After we have used nutrition and first line therapies such as probiotics and digestive support, we can then use antimicrobials (16).

Roots Integrated Care can help

Chronic gut symptoms should not be the status quo. Every week, I see patients who've been suffering from diarrhea, constipation, abdominal discomfort, and reflux for years and decades. If you need professional help by someone who can treat the whole picture and not just one body system, then we can help. You can schedule a free 15-minute Health Strategy Session here.

I hope you found this information useful and helpful in your journey back to a healthier and happier life.

Like what you are reading? Learn more about how to take control of your health by signing up for the "5 Minute Health Makeover" below where I coach you through 3 pivotal strategies for better health.


Resources Cited

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2. Eisenmann A, Amann A, Said M, Datta B, Ledochowski M. Implementation and interpretation of hydrogen breath tests. J Breath Res. 2008 Dec;2(4):046002. doi: 10.1088/1752-7155/2/4/046002. Epub 2008 Jul 24. PMID: 21386189.

3. Ghoshal UC, Nehra A, Mathur A, Rai S. A meta-analysis on small intestinal bacterial overgrowth in patients with different subtypes of irritable bowel syndrome. J Gastroenterol Hepatol. 2020 Jun;35(6):922-931. doi: 10.1111/jgh.14938. Epub 2019 Dec 17. PMID: 31750966.

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11. Rana SV, Sharma S, Kaur J, Sinha SK, Singh K. Comparison of lactulose and glucose breath test for diagnosis of small intestinal bacterial overgrowth in patients with irritable bowel syndrome. Digestion. 2012;85(3):243-7. doi: 10.1159/000336174. Epub 2012 Mar 30. PMID: 22472730.

12. Rezaie A, Pimentel M, Rao SS. How to Test and Treat Small Intestinal Bacterial Overgrowth: an Evidence-Based Approach. Curr Gastroenterol Rep. 2016 Feb;18(2):8. doi: 10.1007/s11894-015-0482-9. PMID: 26780631.

13. Rezaie A, Buresi M, Lembo A, Lin H, McCallum R, Rao S, Schmulson M, Valdovinos M, Zakko S, Pimentel M. Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. Am J Gastroenterol. 2017 May;112(5):775-784. doi: 10.1038/ajg.2017.46. Epub 2017 Mar 21. PMID: 28323273; PMCID: PMC5418558.

14. Shah ED, Basseri RJ, Chong K, Pimentel M. Abnormal breath testing in IBS: a meta-analysis. Dig Dis Sci. 2010 Sep;55(9):2441-9. doi: 10.1007/s10620-010-1276-4. Epub 2010 May 14. PMID: 20467896.

15. Sundin OH, Mendoza-Ladd A, Morales E, Fagan BM, Zeng M, Diaz-Arévalo D, Ordoñez J, McCallum RW. Does a glucose-based hydrogen and methane breath test detect bacterial overgrowth in the jejunum? Neurogastroenterol Motil. 2018 Nov;30(11):e13350. doi: 10.1111/nmo.13350. Epub 2018 Apr 23. PMID: 29687525.

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