Everything You Need To Know About SIBO Testing

Do I Need SIBO Testing?

Do you suspect you might have Small Intestine Bacterial Overgrowth, also known as SIBO? Symptoms might include bloating, constipation, diarrhea, or pain.

If the answer is yes, then your next question should be:

Should I get tested to find out if I really have SIBO?

The short answer is YES.

You might be tempted to move forward with treatment for SIBO without getting tested, but you should know there are 35-40 different diseases that have the exact same symptoms as SIBO. According to Dr. Allison Siebecker, ND, “The symptoms of SIBO are nonspecific.” Just because you are experiencing the symptoms doesn’t necessarily mean you have SIBO. 

It’s very important to know whether or not you actually have it because the treatment for SIBO is going to be very different from other conditions. For example, antimicrobials are typically used to treat SIBO, and because these antimicrobials do have the potential to alter the microbiome of a person, we need to be sure that they are necessary before we move forward. Therefore, it is important to know if a person has SIBO or not.

There are multiple types of testing. There are multiple ways to get tested. And, the outcome isn’t as simple as a “positive or negative” result. In my experience, I have found SIBO breath testing to be the most accurate and the most accessible.

Today, I will share everything I know about SIBO testing with you.

A number of studies have been conducted on how effective you could diagnose SIBO based on symptoms alone, and the results showed it was not at all reliable.


According to Dr. Allison Siebecker, ND, “The symptoms of SIBO are nonspecific. There are maybe 35-40 diseases that could cause the exact same symptoms. Just because you have the symptoms does not mean you have SIBO. And we really need to know because the treatment is going to be different, very different between SIBO to something like lactose intolerance which can cause the exact same symptoms. 

The treatment for SIBO is antimicrobials which potentially could disturb a person’s microbiome. We want to be sure that we need to do those treatments if we’re going to do them. The treatment for lactose intolerance is taking lactase enzyme. We don’t need antimicrobials and changing of the diet. It’s very important to know if a person has it. There have been studies actually done on this now on how well can you diagnose SIBO based on symptoms and it was not well at all.”

Dr. Megan Taylor, ND, agrees: “So, often, we get diagnosed with SIBO after a long journey of having IBS symptoms, and we’re like, ‘Yes, that, that’s it. That must be it.’ And oftentimes, it is. But maybe it’s only a part of it. Maybe it’s only 50% of your symptoms, but the rest are due to something else. And that really needs to be addressed. Just this week, I had an example of somebody who thought it was just SIBO all along. It turned out they had Celiac disease. 

So, you want to make sure that whatever provider you’re seeing is doing that basic work to screen out some of those big conditions that can mimic SIBO—Celiac disease, inflammatory bowel disease, certain particular food sensitivities or food allergies, those sorts of things.”

Not only is treating SIBO potentially damaging if you DON’T have the condition, but assuming it’s SIBO could mean overlooking the real cause of your symptoms. That’s why accurate testing is so important.

Don’t Rely On These Tests For SIBO | SIBO Testing

Inaccurate testing for SIBO is a huge issue! SIBO can only be accurately diagnosed through a breath test or jejunal aspiration during an upper endoscopy.  

According to Drs. Siebecker and Mona Morstein, ND, stool testing cannot diagnose SIBO, but is often ordered anyway. 

“There are a lot of docs who think a stool test could diagnose SIBO just because it’s of the intestines. But it can’t. The stool really represents best the very end of the large intestine. It doesn’t show bacterial overgrowth in a separate organ that’s way up above. The stool test can indicate something about the small intestine but they cannot diagnose small intestine bacterial overgrowth. If you see an overgrowth of bacteria in a stool test that diagnosis is large intestine bacterial overgrowth or LIBO,” Dr. Siebecker said. 

Dr. Morstein seconded this: “We must stop physicians from doing stool tests and saying this has any indication of what’s going on in the small intestine. [The colon] has 500,000 different bacteria. Say that we do a stool test, [saying] we’re reflecting any microbiome in the small intestine is scientifically completely wrong, completely inaccurate.”

Urine organic acids tests are also sometimes mistakenly used to test for SIBO: “I think [the urine organic acids test] is a really cool test. I love it. It indicates all kinds of things but it can’t technically diagnose SIBO. What it can do is indicate some bacterial metabolites, and if they’re in excess we know that there’s too many bacteria and overgrowth. But what it can’t do is distinguish between the large and the small intestine,” Dr. Siebecker said. 

Why Choose Breath Testing For SIBO

For accurate SIBO testing, the most common choice is a glucose or lactulose breath test. Breath tests are non-invasive, and can even be done at home. They’re affordable, even if your insurance won’t cover the test and you’re ordering it yourself.

And most importantly, breath tests correlate with symptoms AND with super-advanced small bowel deep-sequencing being done at research laboratories like Cedars-Sinai, according to Dr. Mark Pimentel, MD. 

“There’s been controversy about breath testing.” Dr. Mark Pimentel said, “People say, “Well, it’s not as accurate as culture” or “We don’t know if it means that…” But we [now] show that SIBO can be proven by deep sequencing—greater than 1000 bacteria per milliliter in the gut is SIBO—and that both of those correlate directly with 90-minute breath tests, meaning the breath test is valid. And the most important thing, they all interdigitate with symptoms. We can correlate with diarrhea, urgency and bloating with these markers.

The point is, for the first time, we’ve internally validated the breath test. Breath tests are valid. And they predict response to antibiotics.”

Watch this video from Gary Stapleton, founder of Aerodiagnostics Labs, to learn more about SIBO breath testing:

Now let’s dive into what “breath testing” really is.

Let’s start with a basic explanation of what breath testing is from Dr. Pimentel:

“When you do a breath test, you drink a sugar. And the sugar we prefer to use is lactulose. It’s a non-absorbed sugar. So it stays in the gut and gets all the way to the colon. So you can get a good flavor of what’s going on in the entire gut. 

When the sugar sees bacteria, they ferment it. When they ferment it, they produce gases. And we look for the gases that humans don’t produce. And the ones we’ve been looking for are hydrogen and methane. Until recently, just those two. 

So, when we see those rise early, meaning within 90 minutes, we know that it’s likely that those gases came from the small intestine.” 

Gary Stapleton, founder of Aerodiagnostics Labs, describes it this way: “What are we doing [with a breath test]? We’re collecting breath to determine, for SIBO testing, whether or not we have bacteria in the small intestine. So how would that possibly work? 

Well, the body, the human body doesn’t produce hydrogen or methane gas. Hydrogen and/or methane gas is only produced by bacteria fermenting or rotting. So what happens, and why we do a preparation for these tests—and we want to be very specific about that preparation because, if you’re not, you can get variable results that don’t match the clinical impressions. 

So, we prep for 24 hours, which is a very specific limited diet; followed by a 12-hour fast, which is typically overnight. It’s convenient for the patient. They wake up. And then, they have a breath collection kit. On a test, they have a collection kit. They’ll collect their breath with a closed capture device.”

Watch this short video (and sneak peek from the upcoming Digestion SOS™ Documentary Series) to see what the collection tubes look like and get tips for accurate testing from QuinTron Instruments (the creators of the equipment used for breath testing). 

You can order glucose breath tests directly from Aerodiagnostics. Lactulose test can be ordered by your physician. 

Interpreting Breath Tests

To put it simply (as Dr. Morstein did), “There is a great deal of grey interpretational area in SIBO testing. Absolutely not is it always clear yes or clear no.”

Once you’ve successfully completed your SIBO test, you might be discouraged to get back a confusing report that you can’t understand (and maybe your doctor is even mystified by it!).

According to Dr. Taylor, “We have to understand that this is not a perfect tool. Breath testing only gives us possible evidence of bacterial overgrowth. We should make sure that our providers who are interpreting our test have a lot of experience doing it or are at least up to date. 

Dr. Rezaie’s team out of Cedars-Sinai published that fantastic breath testing consensus guidelines that came out in 2017. That has been my go-to tool for being able to interpret breath testing in a nuanced way, being able to explain to patients “Gosh! No, your test is definitely positive by all the most conservative reads of the test” or “It’s kind of in that gray area borderline. We should be thinking about what else may be contributing to your symptoms as well.” 

If you need help finding an expert who can interpret a breath test, make sure you check out our list of experts, click here. 

Hydrogen Sulfide & Flat Line Results

Most breath tests look for three gases: hydrogen, methane, and carbon dioxide (as a control). 

Higher levels of hydrogen are correlated with diarrhea, and higher levels of methane are correlated with constipation. But some people also get a “flat line” result – what does that mean? 

According to Dr. Pimentel, it may be related to how hydrogen and methane interact in the intestines, and the presence of a third gas: hydrogen sulfide:

“Some people have a machine that only measures hydrogen. Others have hydrogen and methane.  And then there are people that  don’t even have carbon dioxide. Today, most people have a machine that measures all three. But I’m going to argue that a machine that measures four is even better. And that’s coming in a few more months. Here’s some data on them. 

We can distinguish bacteria [overgrowth] from human by using hydrogen, methane and now the new hydrogen sulfide. And it works like this: hydrogen-producing bacteria feed hydrogen to the methane producers, if you happen to have these characters in your gut. As a result, you produce methane. 

When methane is there and the methanogens are there, they’re eating a lot of hydrogen to make methane. Sometimes,  you get a flat line breath test because they’re eating it all up. They’re just consuming it more than they’re making the methane. But they get energy from this. And this is how the methanogens sustains themselves. They get energy from that. 

Now, the sulfate-producing bacteria, the new characters that we’re looking at, 5 hydrogens on the right to make one hydrogen sulfide, using up all the hydrogen. And this, we were always speculating, could be the flat line breath test because the flat line had no methane, no hydrogen at all, patients were having diarrhea and they were sick. 

And so we now realize that there’s another gas we haven’t done.”

Hopefully, hydrogen sulfide testing will be available within the next year.

Take a Breath!

Phew, I know this is a confusing and complex topic. I hope this post has been a useful resource for you!

If you’re looking for even more information on accurate testing for SIBO, plus treatments, underlying causes, and more – go browse through the SIBO SOS® library of intensive Masterclasses. 


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1 thought on “Everything You Need To Know About SIBO Testing”

  1. Very helpful and timely. I am in the middle of my first SIBO test right now. Thanks to Eric’s video, which confirmed that I am probably doing this right! While I appreciate all of the thorough and complex information and will continue learning, I like that this is a quick guide. Thanks,

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Shivan Sarna

To feel better for longer from bloating, gas, constipation, you need to be empowered with knowledge and inspired to take action. I connect you with the experts, distill the information in an organized and actionable way. This is the information I wish I had when I first learned about SIBO.

kick your digestive discomfort to the curb for good.