What Your Doctor Doesn’t Know About SIBO Breath Testing

Have you asked your doctor for a SIBO breath test and gotten this response, “forget about it, it’s a worthless test?”

When I was conducting my research study on the Specific carbohydrate diet, I was working closely with a GI doctor.

Knowing that SIBO is highly likely in patients with IBS, I asked the GI doctor if we could do a breath test just to provide more information for research purposes.

He told me that he didn’t believe that breath testing was accurate and didn’t recommend it.

This is the belief of many GI doctors as well as physicians and I can see why. I was collecting data for this study in 2014 and the literature did not provide clear guidelines for the use of these tests. Here is a quote from a review article published in 2006 in the journal Gut “regular use of the lactulose breath test in clinical practice in the evaluation of symptoms in patients with suspected functional gastrointestinal disorders cannot be recommended.”1 This was the prevailing thought for many years.

Has all of that changed? Yes!

In 2016, gastroenterologists and research experts met to establish clear Consensus Guidelines to help standardize when to use the breath test, how to prepare for the breath test, and how to interpret it.2 These guidelines were published in 2017.

Despite this, your GI doctor or physician may not feel comfortable with the breath test or isn’t familiar with the new guidelines. So this puts you in a confusing situation. I’m sure you have been reading about SIBO and you’ve learned that the breath test is about the only non-invasive way to measure the presence of SIBO. But here you are at your doctor’s office and they tell you it isn’t necessary or recommended. What should you do?

A Little Background on SIBO Physiology

Before you can understand the ins and outs of the breath test and whether or not you should test, it’s important to know how the test works.

People who don’t have SIBO have less than or equal to about 103 colony forming units (CFU) per milliliter in the upper small intestine.2 That’s about 1,000 living and thriving microorganisms in 0.03 ounces of intestinal fluid. As you move through the 20 plus feet of small intestine the number increases. At the very end of the small intestine going into the colon, the numbers rise to 1012 CFU/mL (which is in the trillions in just 0.03 ounces)!3

People who have SIBO have greater than 103 CFU per milliliter.4 Clinicians can determine this by culturing the bacteria obtained from the upper gut through endoscopy. This procedure  was considered the gold standard up until recently. This type of testing is not practical for the clinical setting and is typically utilized only in a research setting.5 In addition, it is very invasive and there are considerable limitations involved;6 therefore, the consensus guidelines do not recommend this procedure to diagnose SIBO. A better alternative to culturing is using breath tests.

Breath Tests Measure Exhaled Gas from Your Lungs

To conduct a breath test, you blow into a mouthpiece that has a plastic bag attached to it. As you are exhaling, you puncture a vacuum sealed collection tube, which will allow your breath to fill the tube.

It sounds strange-performing a test that actually captures your breath. But is it?

Here is how it works.

If you have bacterial overgrowth, the large numbers of bacteria and/or archaea in your small intestine will produce abnormal amounts of hydrogen and/or methane gases as a byproduct of carbohydrate fermentation. At the beginning of the test, you get a baseline measurement. Then you drink a liquid carbohydrate preparation, which could be either glucose or lactulose, to “feed” the overgrowth. Then you take subsequent measurements over a two to three hour period and the results are graphed and compared to baseline values.

The breath tests used to diagnose SIBO capture and measure the amounts of hydrogen and methane exhaled through the breath. About 80% of these gases are typically expelled through the back end (i.e. farting), but 20% are absorbed through the intestinal wall, pass through the lungs and are exhaled.7

Only bacteria and archeae produce these gases-you do not make them on your own. Because the test is measuring a byproduct of fermentation and not the bacterial numbers themselves, it is considered an indirect measurement.

Are Breath Tests Accurate?

One hundred percent of the 17 gastroenterologists and scientists who developed the breath testing consensus guidelines agreed that breath testing should be used for the diagnosis of SIBO.2

It has been difficult to determine the accuracy of breath testing because studies prior to these guidelines had different cut off points as to what was considered positive or negative results. One clinician would consider a breath test positive for SIBO while another clinician, looking at the same breath test, would consider it negative. There was huge variability in study results mainly because the methodology was not standardized. For example, lactulose breath testing had a specificity (if positive, then you are sure you have SIBO) ranging from 44-100% and a sensitivity (if negative, then you can be certain you don’t have SIBO) ranging from 31-68%.2

In addition, many studies compared the breath test results to the endoscopy culturing results. As I stated above, small bowel culturing isn’t recommended for assessing SIBO and there are many variables that impact the results.

The new consensus guidelines provide cut off values for both hydrogen and methane to help standardize what is considered positive and what is considered negative. Since the guidelines were published, a newer test was developed by Dr. Pimental and group that also measures hydrogen sulfide. This test is called the Trio-smart breath test. Still, it is difficult to find a medical test that is 100% accurate and many factors are involved that can impact the accuracy of the breath test.

There are certain things that you, the person conducting the breath test, can do to make the results more accurate. Carefully following these instructions that were outlined by the consensus guidelines when preparing for the breath test can help:

  • Avoid antibiotics for 4 weeks prior to the breath test
  • Promotility drugs and laxatives should be stopped at least 1 week prior to testing
  • Fermentable carbohydrates and smoking should be avoided the day before testing
  • The person should fast at least 8 hours prior to the test
  • Physical activity should be limited while conducting the test

To the relief of practitioners and their patients, the guidelines recommended that it wasn’t necessary to stop proton pump inhibitors (acid blockers) prior to testing.

One of the hardest things that my clients complain about is having to avoid fermentable carbohydrates 24 hours before the test. You have to follow a very simple diet, for example, just some plain animal protein and white rice. Failing to do this can increase chances of a false positive (the test detecting SIBO when you don’t really have it). Detailed instructions are provided in every breath test kit and following the guidelines will help you get better results.

Which Carbohydrate Source is Best?

In order to feed the bacteria to encourage them to produce gas, a measured amount of carbohydrate will need to be ingested. Breath tests offer two different carbohydrate sources for this purpose, glucose or lactulose. Both have their pros and cons. For example, glucose is absorbed higher up in the intestinal tract, so it may miss someone with an overgrowth in the lower part of the small intestine. However, if it is positive, then there is a high certainty that the person has SIBO.

On the other hand, lactulose breath tests are more sensitive than glucose, meaning a negative result will indicate that the person doesn’t have SIBO,6 but there is a much higher incidence of false positives, and here is why:

  • Lactulose isn’t absorbed in the small intestine like glucose is. If you are looking at the timed graph and you see the numbers increase, you aren’t certain if the lactulose is still in the small intestine or if it has arrived in the large intestine. Once the lactulose is in the large intestine, the numbers will rise significantly. Fermentation in the large intestine could falsely elevate the results on the breath test. Remember, we want to know if fermentation is happening in the small intestine, not the large intestine.
  • Lactulose also increases transit time, meaning it may reach the large intestine too quickly, making it look like the person has SIBO.

The  consensus guidelines recommend to look at the rise in hydrogen above baseline by the 90 minute mark on the graph. This will help reduce false positives. It is also important that the practitioner understand the patient’s usual bowel habits (do they typically have diarrhea or constipation) while interpreting the test.

There is one company that I know of that is offering both carbohydrate substrates in one test. That is very handy but also makes the test more expensive. From speaking with other practitioners, the majority prefer to use lactulose.

I prefer lactulose over glucose because I think it is better to treat SIBO (even if you truly didn’t have it) than to withhold treatment if a glucose breath test was negative-when you really do have SIBO. SIBO can cause devastating symptoms and not treating it can prolong suffering. Plus, treatment for SIBO has less risks as opposed to the benefits of getting rid of SIBO.

My Doctor Wants to Treat Without Testing

Testing for SIBO has been fraught with controversy and many doctors have been distrustful of using breath tests. If your doctor isn’t aware of the different substrates, how to interpret the test, what the patient needs to do to prepare for the test, and all of the other ins and outs of the test, they simply may not feel confident with breath testing. Instead, they will treat empirically, meaning prescribing the treatment without confirming the diagnosis. If the symptoms go away with treatment, then that is confirmation of SIBO. This way of thinking can have value. It can save the patient money and time, but there are also cons to this as well, which I will explain below.

Treating empirically is necessary sometimes. For example, I had a client (we will call her Mary),  who was desperate. She was underweight because eating was just too painful. Her bloating was so bad that she looked 6 months pregnant. She also had bouts of diarrhea. Upon further investigation, it was found that her severe bloating happened after eating high FODMAP foods. This was suggestive of SIBO. The problem was, Mary didn’t have time to conduct a breath test because in 5 days she was going on a cruise. She wanted to enjoy her cruise and not be plagued with bloating and pain. I asked that she see her doctor about starting a course of rifaximin in hopes that she would get enough relief in time to enjoy her cruise. Within 3 days of taking the rifaximin, she told me that the bloating and pain had significantly subsided. She emailed me later to tell me what a great time she had on her cruise.

This is a case where treating a patient without testing made sense and in fact, many practitioners will go this route.

As far as cost, breath tests costs a couple of hundred dollars, more or less. Ideally, you want to retest after treatment. This can add up. Some patients just can’t afford the test.

On the other hand……

Reasons Why You Should Consider Testing

Why should you test? First, it is difficult to distinguish SIBO from other conditions that can cause diarrhea, bloating, abdominal pain, excessive gas and nausea. Therefore, it is recommended that an accurate diagnosis is made before treating.6 I have had clients that I was sure that they had SIBO, but their lactulose breath test was negative. In that case, we were able to focus on other causes. Testing can save time and money in the long run by preventing you from going in the wrong direction.

Second, it is helpful to know what type of SIBO you have, since there are different types. The breath test can tell if you are hydrogen or methane dominant (and hydrogen sulfide if using the Trio-smart breath test), and this is important to know since they have different treatments. To read more about the different types of SIBO, see: Do You Know Your SIBO Type?

Third, it is helpful to know if the treatment that you adopted actually reduced or eliminated the SIBO (by conducting a retest) or if you need to try another treatment option. Again, it can take more time and money to guess at what you have vs. actually knowing.

Should You Test or Treat Without Testing?

To answer this question, you will need to think about your situation and make a decision together with your practitioner.

I treated my suspected SIBO for about a year with various herbs before I finally decided to actually see what was going on in that intestinal tract of mine. For me, it was so revealing to get my breath test back and see the huge amount of methane gas that my test revealed. Finally, there it was-I could definitively say that I had methane dominant SIBO. I learned from retesting what treatments it took to get a negative test and at what gas level I actually felt symptoms. For example, I can tolerate methane levels of around 30 ppm and feel fine, but when they rise above that, I feel terrible. Testing and retesting helped me fine tune my treatment and figure out my goals.

I feel that it is better to know what you have than to guess; however, every individual situation is different. You need to make that call along with your practitioner’s guidance.

The 2017 consensus guidelines have really helped standardize the breath tests. However, like many tests, breath tests still have to be properly interpreted by a skilled practitioner.

I have taken numerous trainings on how to read and interpret breath tests and I utilize them on the majority of my clients. Please click here if you would like to have a free 30 minute SIBO Troubleshooting Session. During this session we can discuss your individual situation and whether or not SIBO breath testing is right for you.

If you are working with a physician who is interested in breath testing, but just needs further guidance, then please download the Consensus Guidelines and bring it to them to read.


  1. Simrén M, Stotzer P-O. Use and abuse of hydrogen breath tests. Gut. 2006;55(3):297–303. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1856094&tool=pmcentrez&rendertype=abstract.
  2. Rezaie A, Buresi M, Lembo A, et al. Hydrogen and methane-based breath testing in gastrointestinal disorders: The North American consensus. Am. J. Gastroenterol. 2017;112(5):775–784. Available at: http://dx.doi.org/10.1038/ajg.2017.46.
  3. Adike A, DiBaise JK. Small Intestinal Bacterial Overgrowth: Nutritional Implications, Diagnosis, and Management. Gastroenterol. Clin. North Am. 2018;47(1):193–208.
  4. Ghoshal UC, Ghoshal U. Small Intestinal Bacterial Overgrowth and Other Intestinal Disorders. Gastroenterol. Clin. North Am. 2017;46(1):103–120. Available at: http://dx.doi.org/10.1016/j.gtc.2016.09.008.
  5. Eisenmann A, Amann A, Said M, Datta B, Ledochowski M. Implementation and interpretation of hydrogen breath tests. J. Breath Res. 2008;2(4):046002. Available at: http://www.ncbi.nlm.nih.gov/pubmed/21386189 [Accessed March 2, 2013].
  6. Saad RJ, Chey WD. Breath testing for small intestinal bacterial overgrowth: Maximizing test accuracy. Clin. Gastroenterol. Hepatol. 2014;12(12):1964-72; quiz e119–20. Available at: http://www.ncbi.nlm.nih.gov/pubmed/24095975 [Accessed August 29, 2018].
  7. Ghoshal UC, Shukla R, Ghoshal U. Small intestinal bacterial overgrowth and irritable bowel syndrome: A bridge between functional organic dichotomy. Gut Liver. 2017;11(2):196–208. Available at: http://www.ncbi.nlm.nih.gov/pubmed/28274108 [Accessed April 15, 2018].

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