What is the Best Test For SIBO - Dominick Hussey

What is the Best Test For SIBO?

There is a lot controversy over what is the best test for SIBO. This debate is the big problem when it comes to SIBO, in my opinion.  We treat many people for SIBO, and indeed, if they do have SIBO and it’s causing their symptoms, that’s appropriate and important, but it is critical to be aware of some of the realities around the testing of SIBO.

In this article, I am going to review all of the conflicting evidence and viewpoints and tell you what in my opinion is the best test for SIBO.

Current SIBO Testing

There are currently two primary tests for SIBO. One is an endoscopy with bacterial culture, where they measure the levels of bacteria. The second one is a breath test. Both tests have their advantages and disadvantages.

Endoscopy with Bacterial Culture

Endoscopy with bacterial culture is the most direct method of testing for SIBO.  This approach counts the number of bacteria in the small intestine, but there are a lot of problems with this process.

The first problem is that you have to intubate the small intestine. With Intubation we pass a catheter into the distal duodenum through an endoscope and fluid is aspirated for culture. This procedure is a very invasive procedure, costly, and it involves some risk.

The second issue is that many of the species that inhabit the small intestine cannot efficiently be cultured. As a result, any quantitative culture will underestimate the number of bacteria in the small intestine.

Thirdly, the contamination of the endoscope and catheter can occur as we pass the instrument through the digestive tract. Contamination can cause problems for the patient and also affect the test result.

Fourthly, SIBO is known to be patchy in distribution. So let’s say they take a sample of an area of the small intestine where there isn’t any bacterial overgrowth, and that returns a negative result.  That area may have been right next to a slice of the small intestine that did have bacterial overgrowth.

Lastly, accurate results require prompt and proper specimen handling.

All of these shortcomings explain why endoscopy is rarely used now in clinical practice for SIBO testing. Endoscopy is only used in research settings at this point, and even then not so much.

Breath Testing

All of the various challenges of using endoscopy have led to the development of a different method of testing for SIBO, namely breath testing.

Breath testing is non-invasive, safe, simple to perform at home, and relatively cheap compared to the endoscopy.

Breath testing is far more commonly used, especially in functional medicine, and does indeed have advantages over culture, but it’s far from perfect, and there are some problems.

  1. There is no consensus about what substrate is best to use during the testing. Some argue that glucose is best, others say that lactulose is best.
  2. There is no consensus about how to interpret breath tests.
  3. Differences in bacterial flora in patients can affect test results. For example, 10 percent of adults and 15 percent of kids don’t produce hydrogen at all, they only generate methane, so if you’re not testing for methane, you’re going to miss those people. And some people don’t produce much hydrogen or methane at all, and they produce more hydrogen sulfide, and that’s not measured on any of the current breath tests, so that’s a problem.
  4. The optimal protocol for timing, collection, and method of administering breath tests is not known or agreed.
  5. Recent antimicrobial use before testing might affect results, but the proper antimicrobial-free interval before doing the test is not known. A commonly used range is two weeks, but there haven’t been a lot of studies done to establish what the proper interval is.

In short, the breath test is an easy test to perform, but it’s difficult to interpret the results.

What is the best substrate to use in SIBO Breath Testing?

I mentioned above that each of the substrates that are used clinically, lactulose and glucose primarily at this point, has its pros and cons, so let’s start with glucose.


The main problem with glucose is that it’s absorbed in the proximal small intestine and the duodenum, so if overgrowth of bacteria is occurring in the jejunum or ilium, you may get a false negative with a glucose breath test. That said, the Rome Consensus Conference recommends glucose breath testing over lactulose breath testing. The glucose test has a positive predictive value of 80 percent and a negative predictive value of 66 percent, versus a positive predictive value of 62 percent for lactulose and a negative predictive of 54 percent for lactulose. And regarding diagnostic accuracy, glucose breath testing is 72 percent versus 55 percent for lactulose breath testing.


Lactulose, on the other hand, in contrast to glucose, is not absorbed in the small intestine. Lactulose goes all the way to the colon, where bacteria ferment it.

The advantage of lactulose breath testing, therefore, is that it can detect SIBO if it’s happening in the middle or lower part of the small intestine.

The biggest problem with lactulose as a substrate is that the lactulose breath test is based on the idea that it takes a certain amount of time (transit time) for the substrate to go from the mouth to the first part of the colon. In healthy people, labs assume, this transit time is always 90 minutes.

Therefore, most labs that do breath tests interpret any rise in hydrogen over a specific cutoff that happens before 90 minutes as a positive result for small intestine bacterial overgrowth.

However, there is a problem with this assumption idea because studies have shown that the transit time in healthy people averages 72 to 85 minutes.

  • A study in India found a median transit time of 65 minutes in healthy people.
  • A study in Taiwan found a median transit time of 85 minutes.
  • One recent study in Western populations radio-labelled lactulose so that they could measure the progress of it as it moved through the gut while they were doing the SIBO test.  This study showed a high percentage of people with IBS had an early peak of hydrogen, but before 90 minutes on the lactulose breath test. But in 88 percent of cases, the lactulose had already reached the colon. So in other words, this was an 88 percent false positive rate. There was a high percentage of patients showing an early peak before 90 minutes in hydrogen. Virtually all labs would interpret this result as positive for SIBO. But they knew in the study from radiolabeling the lactulose that it had already reached the colon in 88 percent of these cases. In which case it wouldn’t be indicative of SIBO, it’s just a typical rise of hydrogen production that we would expect when lactulose enters the colon.

Further complicating this problem of transit time is that lactulose has a laxative effect. In fact, lactulose was commonly used as a laxative for kids who had constipation. It accelerates transit time so that the lactulose will reach the colon in less than 90 minutes, and that could generate a false positive.

There are a few studies that have compared lactulose breath testing with glucose breath testing directly, in both IBS patients and controls.

The studies found that SIBO is present in 34 percent of IBS patients if you use the lactulose breath test, but only 6 percent of patients using the glucose breath test.

The numbers in controls were even more dramatic. Using the lactulose breath test, 30 percent of healthy controls had SIBO versus just 0.7 percent with glucose breath testing.

SIBO was not statistically different in patients with lactulose breath testing, but it was statistically different in IBS patients and controls with glucose breath testing.

So, put another way, only glucose breath testing was able to distinguish between IBS patients and controls, whereas lactulose breath testing was not able to differentiate between them.

So I know that this might be a little overwhelming or confusing, so let me bring all of it together for you.

Glucose breath testing favours specificity over sensitivity. So if you choose glucose breath testing, you’re accepting a higher possibility of false negative in the case of SIBO that’s happening in the middle or lower parts of the small intestine, and you’re erring toward undertreatment rather than overtreatment.

So, glucose breath testing has more diagnostic accuracy than lactulose breath testing.

On the other hand, lactulose breath testing favours sensitivity over specificity. There’s a higher possibility of a false positive, especially if the patient has normal or faster-than-normal transit time.

So here you are erring toward overtreatment, and overall, there’s less diagnostic accuracy than glucose breath testing.

So with all of this in mind, what is the best test for SIBO?

The best test for SIBO is lactulose breath testing. That might be somewhat surprising given what we’ve covered regarding the overall lower level of diagnostic accuracy of lactulose compared to glucose breath testing.

The reason I use lactulose is that I think the risk of undertreating SIBO is higher than overtreating. The treatments for SIBO, whether you are using herbs, or antibiotics for SIBO, are both remarkably safe and aren’t likely to cause a lot of side effects, complications or risks.

I think the potential benefits of treatment far outweigh the potential consequences because of the safety of the treatment interventions.



This article is not intended to provide medical advice, diagnosis or treatment.

Now I’d like to hear from you. Let us know in the comments below.


Like what you’ve read? Sign up for FREE updates delivered to your inbox.

* indicates required


Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.