How to Test for Small Intestinal Bacterial Overgrowth (SIBO)

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A SIBO breath test can reveal if your chronic intestinal symptoms are caused by small intestinal bacterial overgrowth (SIBO). Jejunal aspiration—the removal and culture of a sample of intestinal fluid—is less commonly done, but is a more accurate SIBO test.

Research suggests SIBO is underdiagnosed. You should be tested for it if you have ongoing bloating and bowel problems. Treatments for SIBO are available, so identifying it can open the door to symptom relief.

In this article, you'll learn about each testing option, what to do before the test, and what to expect from the test itself.

Doctor holding endoscope
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Who Should Be Tested?

Experts recommend SIBO testing if you have chronic:

  • Bloating
  • Abdominal pain
  • Diarrhea

This is because irritable bowel syndrome (IBS) can be misdiagnosed in people with these symptoms.

Testing is also recommended if you have:

The diagnostic tests for SIBO are breath tests, jejunal aspiration, and a medication trial.

SIBO Breath Test

Breath testing is non-invasive. It's used fairly frequently as a way to look for SIBO.

When bacteria in the small intestine interact with sugar, they release hydrogen or methane. Those chemicals then come out in your breath.

For the test, you consume a sugary drink and then have your breath checked periodically. If hydrogen is detected before the 90-minute mark, it suggests SIBO.

Bacteria that produce hydrogen belong in the large intestine, not the small one. It takes about two hours for the sugar to reach the large intestine. That's why the cutoff is 90 minutes.

Despite wide use, some experts have concerns about the validity of SIBO breath tests. Unfortunately, the breath test is not very accurate and yields many false-positive results, especially in people who digest food faster than average.

There are two types of breath tests: One uses glucose and the other lactulose. Of the two, the glucose test seems to be better. But both are often inaccurate. The sensitivity and specificity of the tests range from 44% to 83%.

The test can also produce false negatives. That's often because of gastroparesis (slow emptying of the stomach).

In addition, there's no consensus on how best to perform the test. Nor is there agreement on exactly what amounts of gas should be present for a positive result. Still, the simplicity and safety of the test make it a popular way to test for SIBO.

  • Non-invasive

  • Easy to do

  • Safe

  • Many false results

  • No agreed-upon protocol

  • No standard for a positive result

  • Intensive preparation

  • Time consuming

Before the Test

Testing should be done at a clinic or lab that tests for both hydrogen and methane. Your healthcare provider or the facility will tell you how to prepare.

Follow directions carefully so you get accurate results. Typical guidelines are:

  • In the month before: Do not use any colon cleansing products like what's used before a colonoscopy.
  • In the four weeks before: Don't take any antibiotics or probiotics.
  • In the week before: Don't use laxativesfiber supplements, or stool softeners.
  • In the 48 hours before: Avoid high carbohydrate meals and snacks, especially whole grain bread or pasta.
  • GERD medication for 48 hours before: If you take prokinetic medications (Cisapride, Motegrity) for gastroesophageal reflux disease (GERD), you may need to go off of it.
  • In the 12 hours before: Don't smoke, exercise, or eat or drink anything. This includes gum and candy.

During the Test

During the test, you may be asked to rinse your mouth with mouthwash. That kills any bacteria that may be present.

You'll then give a baseline breath sample. Usually, that means blowing up a balloon. Then you'll drink a small amount of sugary liquid.

Every 15 minutes, you'll give them another breath sample. The test will last two to three hours, depending on the type of sugar used.

Jejunal Aspiration

A more accurate test—but also more invasive—is jejunal aspiration. It takes place during an upper endoscopy procedure.

An upper endoscopy involves a long tube with a camera threaded down through your mouth and throat. It's named for the middle section of your small intestine: the jejunum.

During the endoscopy, the practitioner can take a sample. It's then cultured and evaluated for bacteria.

Jejunal aspiration isn't used often. It's costly, time-consuming, and carries more risk than a breath test—although it's generally considered safe.

Jejunal aspiration has limits to its accuracy for SIBO. False negatives are possible when:

  • The sample is taken from an area where the bacteria aren't overgrown.
  • The sample isn't large enough.
  • The culture used was the wrong one for your particular bacteria strain.
  • The sample was tainted by bacteria in your mouth, on the instruments, or through poor handling.

Despite these limitations, many researchers consider jejunal aspiration the "gold standard" for SIBO testing.

Before the Test

Your healthcare provider or the testing center will tell you how to prepare. Those instructions will likely be similar to those for the breath test.

If you have gastroparesis, you may be told to follow a liquid diet for three days before the test.

During the Test

The test will take place either at your healthcare provider's office or at a testing facility.

Monitors may be placed on your body so your provider can keep an eye on your breathing, heart rate, and blood pressure.

An IV will most likely be started. You'll get a mild sedative to relax you. It may not put you fully out.

Next, a numbing anesthetic will be sprayed on your throat. Then a thin tube will be inserted down your throat.

You'll be able to breathe but not talk. Your healthcare provider will then take a sample of fluid from your small intestine using an aspiration catheter.

Then the tube will be removed from your throat. After that, you may rest for a while to allow the anesthesia to wear off.

Because you'll be sedated, you can't drive yourself home afterward. For the rest of the day, keep your activity to a minimum.

You may have mild side effects such as:

  • Gassiness
  • Bloating
  • Cramping
  • Soreness in the throat area

If you experience any severe, unusual, or worrisome symptoms (vomiting or coughing up blood), contact your healthcare provider immediately.

Medication Trial

One way to check for SIBO is with a trial of SIBO medication. If symptoms quickly drop off, it suggests you have it.

The most common SIBO drug is Xifaxan (rifaximin)—an antibiotic. It's different from most antibiotics, though. Rather than being absorbed into your bloodstream, it acts directly on bacteria in your small intestine.

The medical community hasn't yet set dosing standards for SIBO trials. But some healthcare providers follow the FDA guidelines for using Xifaxan to treat diarrhea-predominant IBS (IBS-D).

These guidelines recommend taking the medication for a two-week period, then repeating it for another one or two weeks.

This approach has limits, though.

  • There's no guideline as to what's considered a "good" response.
  • If you don't get enough to kill the bacteria, the trial may be inconclusive.
  • Too much medication can result in side effects.

So this approach is a tricky one to gauge.


SIBO may be underdiagnosed. If you have ongoing bowel problems, you should be tested.

Three types of SIBO testing are used:

  • Breath tests for hydrogen or methane
  • Jeujunal aspiration during upper endoscopy
  • A trial of Xifaxan

Each approach has pros and cons for diagnosing SIBO.

7 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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  5. 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. doi:10.1038/ajg.2017.46

  6. El kurdi B, Babar S, El iskandarani M, et al. Factors that affect prevalence of small intestinal bacterial overgrowth in chronic pancreatitis: a systematic review, meta-analysis, and meta-regression. Clin Transl Gastroenterol. 2019;10(9):e00072. doi:10.14309/ctg.0000000000000072

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Additional Reading

By Barbara Bolen, PhD
Barbara Bolen, PhD, is a licensed clinical psychologist and health coach. She has written multiple books focused on living with irritable bowel syndrome.