SIBO Testing and Fine-Tuning Issues

From the holistic medicine viewpoint and Science, there are many questions unanswered and even dogmas in the standard of care. Below a few issues.

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Issue One: Is lactulose breath testing an accurate way to diagnose SIBO?

The standard way of diagnosing SIBO in an outpatient setting is using lactulose breath testing, but this test is not accurate. There is another way, which is an endoscopy, where medical doctors put a tube down your throat and take a sample of bacteria from your small intestine, but that’s never used in outpatient settings because it’s invasive and expensive.

Because over 90 percent of the patients that are normally tested for SIBO test positive, there is doubt.  By using the machine-generated criteria that are printed on any of the SIBO breath testing labs. This is a red flag because usually many of these patients dont have SIBO.

None of these tests are gold standards. This is why in Holistic Medicine, we use as few tests as possible and get to feel good solutions.



acne rosacea had SIBO [Correction: study I was referring to found that SIBO was 17 times more prevalent in patients with rosacea than in controls.]

over-diagnosing SIBO.

Changes in criteria

Now I mentioned the criteria, so up until pretty recently the idea was that if you see an increase in 20 parts per million or more of hydrogen in the first 120 minutes of the test, that would indicate a positive result, and the criteria were an increase in 12 parts per million for methane, but those criteria recently changed; there was a consensus statement issued in the spring.


A bunch of SIBO experts got together and talked about how to update the breath-testing criteria to make it more accurate and ensure that the criteria were modified to, on the one hand with hydrogen, the changes would lead to fewer diagnoses, less overdiagnosis of hydrogen-predominant SIBO. But in the case of methane, they’re going to lead to a greater number of diagnoses because those criteria, instead of becoming more strict, became more liberal. The new hydrogen criteria are increasing 20 parts per million within the first 90 minutes, and then with methane, it’s any value over 10 parts per million at any point during the test, including during the third hour. That’s a pretty big difference, and that’s going to lead to a lot more positive results for methane.

It’s also worth pointing out that there are a lot of different studies that are critical of lactulose breath testing that suggest that there is a very high potential for false positives, especially using lactulose instead of glucose. With glucose breath testing, the opposite problem is true. There’s a high potential for false negatives. If there is a positive, it should be positive. But if there’s a negative, you can’t rule out that SIBO might be present. Again, I’m not going to go into great detail here, but let’s just say that there is a lot of uncertainty about breath testing as a way of diagnosing SIBO.

Hydrogen/Methane Breath Test

The challenges of jejunal aspiration led to the invention of another type of test called the hydrogen breath test. It is the most popular way to diagnose SIBO due to its low risk, simplicity, and noninvasive nature.

The test involves the patient fasting overnight and then eating a sugar that is fermented by the bacteria in the small intestine. The gases from the bacteria are then captured and used to see if there is an overgrowth [R].

HBT has its drawbacks. In about 15-30% of people with SIBO, the bacteria will produce methane instead of hydrogen [R].

It is necessary to also test for methane if the hydrogen breath test is negative. People who test positive for methane tend to have constipation [R,R,R].

The HBT also has a high false negative rate. This means that the test turns up a negative result when in fact the person does have SIBO [R].

Lastly, there is no consensus as to what determines a positive result. The only way of being confident in the results is to treat SIBO and see if symptoms disappear [R].

Despite these drawbacks, most doctors still prefer the use of the HBT [R].

Some practitioners even prefer using stool or urine testing (organic acids), but there isn’t any scientific support for these tests.

Hydrogen breath tests can be administered by a gastroenterologist. They can also be purchased online and performed in the comfort of your home. Results are sent into a lab to be tested for the presence of SIBO.

Sampling The Small Intestine

The gold standard for SIBO testing is jejunal aspiration. This involves taking a sample from the small intestine and counting the number of bacteria per mL.

It is a costly and invasive procedure that requires a tube to be inserted into the small bowel. Another issue is the risk of contamination of the tube as it is passed through the stomach [R]


Issue Two: Is SIBO always pathological?

The second assumption is that SIBO is always pathological. The idea is that if SIBO is present, it’s always causing the patient’s problems, whatever they are, but that’s not sound thinking, of course, because we know that correlation is not causation. It’s possible that SIBO could be present, but it’s not actually driving whatever the patient’s symptoms are. We know that early studies suggested that up to 20 to 30 percent of healthy controls have SIBO but don’t have symptoms. Of course, I have to offer a side note here, which is, I don’t know where these studies are finding these so-called “very healthy controls with no symptoms.” I haven’t met that many of those people, but let’s assume that that’s true. That could mean that 20 to 30 percent of the population has SIBO, but it’s not causing any problems for them.

In many cases, we treat SIBO, and the numbers improve, so the patient goes from being breath-test positive to breath-test negative, but their symptoms don’t necessarily improve. That would suggest that maybe SIBO was present, but it wasn’t causing their symptoms. It’s possible that the testing is accurate as far as what it’s measuring, but what we call SIBO as a condition is not always pathological. It’s also possible that SIBO might be present in a patient and might be causing some issues, maybe a mild nutrient deficiency or something like that, but it’s not causing the main complaints.

The reason I bring this up is that I see some patients just getting hyperfocused, almost obsessed about SIBO, at the expense of everything else. And clinicians—there is that saying, “If you’ve got a hammer, everything looks like a nail”—I see both clinicians and patients becoming over-focused, I think, on SIBO, and the risk there is that you actually miss other pathologies or underlying mechanisms that are really actually driving the condition in those cases if we’re just myopically focused on SIBO.

Issue #3: Are our treatments effective?

The third assumption is that our current treatments are effective and optimal. The typical treatments for SIBO are antimicrobials. Initially, there were prescription medications. Rifaximin is the most commonly used, especially for hydrogen-predominant SIBO, and neomycin is also added at times when methane is present. Metronidazole is another medication, or Flagyl is used in some cases for treating SIBO, as well as other antibiotics, but rifaximin certainly has become the drug of choice. But then there have been some studies recently that have found that botanicals, herbs, are as effective as rifaximin treatment or even more effective and cause fewer side effects. In general, the approach is if SIBO is there, then you use antimicrobials to reduce the growth of bacteria in the small intestine.

The problem with this approach is that the efficacy is often quite low. I’ve seen some studies that we use rifaximin individually that show as low as 40 percent efficacy. Of course, there are other studies that show higher efficacy, and then if you combine other agents in the treatment, you can make it more effective. There was one treatment where the researchers speculated that using partially hydrolyzed guar gum would improve the efficacy of rifaximin, and in fact it did. It increased it significantly. In our clinic we use a combination protocol that uses a bunch of different things together, all of which are designed to maximize the efficacy. It also depends whether it’s just hydrogen alone that’s high, or methane alone that’s high, or both hydrogen and methane, and each of those scenarios requires a different approach.

But the problem remains that efficacy is much lower than I certainly would like to see it. Not only that, in some cases, not only do patients not get better, they actually get worse after treatment. They might get worse right away or they might improve initially, but then the symptoms return and when they come back, they come back even worse. I’ve seen this actually happen in multiple cycles, meaning with each treatment and each return of symptoms, the symptoms get worse after each cycle, which is obviously problematic.

Then there’s the very high rates of recurrence for SIBO, which is related to what I just said. One study, I think, found a recurrence rate of 45 percent in patients who had been treated by rifaximin. In our practice, despite using all of the evidence-based methods and combining several different methods, we still see recurrence rates a lot higher than optimal, than I think is acceptable. That’s one of the main things that has led me to question many of these beliefs and assumptions because when the treatments are not that effective and the recurrence rates are very high, then I think that something is definitely wrong.

ISSUE #4: Is SIBO always the underlying cause?

The fourth assumption is that SIBO was always the underlying cause of a particular condition. This is somewhat related to what I mentioned earlier, but a little bit different. In functional medicine, we’re always trying to get to the root of the problem, but sometimes that’s easier said than done, and it can be like peeling layers of an onion back to keep going deeper to find the deepest underlying issue. If a patient has SIBO, for example, and we treat their SIBO and it doesn’t go away, or maybe it does go away and it comes back, and we do that two or three times, then of course I start wondering, “All right. Well, is there some other deeper condition that is causing the SIBO?”

In this case SIBO is not necessarily a cause itself, but almost a symptom of a deeper underlying problem. In my experience, those problems can be things like:

•mold or chronic inflammatory response syndrome

•chronic infections like tick-borne illnesses

•viral reactivation

•other gut infections that have escaped detection

•heavy metal toxicity

•other types of toxicity

•mitochondrial deficiency

And a range of other problems. But the point being that in those cases, those problems are the real thing that’s driving SIBO and then whatever symptoms the SIBO is causing. It’s like layers, and so you have to keep going deeper in order to identify and address those conditions, otherwise that patient is never going to get over SIBO. We’ll just keep treating it, it might improve a little bit or not, and then it just keeps coming back. Even though rifaximin and the botanicals are relatively safe compared to other antimicrobials, they’re still antimicrobials, and we still want to minimize our use of them.

Issue #5: Should probiotics and prebiotics be avoided during treatment?

Assumption number five is that probiotics and prebiotics should always be avoided when a patient has SIBO and shouldn’t be included in treatment. I think I’ve discussed this before and I’m not totally sure where this belief or assumption came from. It’s pretty prevalent within the mainstream SIBO community, if you want to call it that. But all of the studies that I’ve seen, I think, without exception, have found that when you use probiotics, either along with antibiotics or as a separate distinct treatment for SIBO, they are effective. They’re either effective as solo treatment, or they increase the efficacy of SIBO [treatment protocols]. Even the studies that have used prebiotics have shown positive results, which might be a little counterintuitive because you would expect prebiotics to feed the bacteria that are present in the small intestine. I think there are still quite a few questions here. Certainly, I have seen probiotics and prebiotics make patients with SIBO worse, but in other cases, I’ve seen them make patients with SIBO significantly better. We do include very specific types of probiotics and even prebiotics in our SIBO treatment protocol. We’ve done that for many years because of the research I’ve seen on this, and I do think it is effective in most cases.

This sort of points to another question or concept, which historically a lot of SIBO authorities have claimed that SIBO is just really kind of a small intestine, it’s not really related to the health of the large intestine or the overall gut microbiome. That doesn’t make sense to me. There is a sphincter that separates the small and large intestine, but one of the prevailing theories about how SIBO got started in the first place is it’s an inappropriate transfer of bacteria from the large intestine to the small intestine. It’s entirely possible, and even likely, in my opinion, that one of the predisposing factors that can lead to that translocation of bacteria from the large intestine to the small intestine is an unhealthy large intestine. It may be that that’s one of the reasons that prebiotics and probiotics work in terms of treating and even preventing recurrence of SIBO is that they help to improve the gut microbiome. That, in turn, has a sort of upstream effect on the small intestine. Really, still a lot of unanswered questions here related to probiotics and probiotics, but I’ve seen enough now to convince me that the dominant idea that they should always be avoided is not true.

Question #6: Does a long-term low-FODMAP diet help prevent recurrence?

Then finally, the last assumption, number six, is that a long-term low-FODMAP diet is always a good idea in order to prevent recurrence. I have discussed this and written about this before, so I’m just going to mention it briefly. But studies have shown that a long-term low-FODMAP diet can reduce the diversity and quality of beneficial bacteria in the large intestine, and for the reasons that I just mentioned, I think that that can be problematic. Even though the low-FODMAP diet can reduce symptoms, it may be setting patients up for recurrence if it’s leading to undesirable changes in the beneficial bacteria in the colon. Also, there was a recent study that just came out that found that patients with IBS are often able to reintroduce certain FODMAPs without any adverse effects. This study didn’t consider SIBO, but as you probably know, many patients with IBS do have SIBO. My guess is that they would have found a similar effect if they had done the study in patients that only had SIBO. It seems that even in patients who do have SIBO or IBS that reintroducing some FODMAPs not only could be potentially beneficial, but doesn’t actually lead to a return of symptoms. That’s what I’ve always encouraged my patients to do is reintroduce as many FODMAPs as they can without significant discomfort. I think that’s a wise approach because we want to keep our diet as diverse as possible, and especially when it comes to fermentable fiber, it can support our beneficial gut bacteria.

I think it’s a very important starting place to just admit when we don’t know the answers to these questions at least, and to lay those questions out so we can start exploring what the answers might be, and of course that is the process of science.

It’s not that we always have the answers and we always know what and we stop looking. Once we think we know the answers, we always question our assumptions and we continually re-evaluate them, especially in the face of evidence that contradicts our previous assumptions or beliefs. That’s the true application of the scientific method in the case of healthcare.

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