How to Get Tested for Small Intestinal Bacterial Overgrowth (SIBO)

Technician performing Endoscopic exam

Air Rabbit / Getty Images

Have you or your doctor considered the diagnosis of small intestinal bacterial overgrowth (SIBO) as an explanation for your chronic intestinal symptoms? Emerging research suggests that SIBO is an under-diagnosed condition whose presence should be identified or ruled out for individuals who are experiencing ongoing bloating and bowel problems.

As there are treatments available for SIBO, identifying its presence opens the door for symptom relief. Your doctor has three primary options to recommend to you for diagnosing SIBO. Here you will learn a little about each option, what you will need to do prior to the test to improve its accuracy, and what to expect from the test itself.

Who Should Be Tested?

Due to the concern that many people are misdiagnosed as having ​irritable bowel syndrome (IBS), researchers are recommending that anyone who is experiencing chronic symptoms of bloating, abdominal pain, and diarrhea should be tested for SIBO. SIBO should also be ruled out for anyone who is showing signs of nutritional deficiencies.

SIBO testing is also recommended for anyone who is experiencing a worsening of symptoms of the following health conditions in spite of adequate medical treatment: chronic pancreatitis, Crohn's disease, and scleroderma. SIBO testing also is recommended for anyone who has celiac disease, but who continues to experience symptoms despite strict adherence to a gluten-free diet.

Breath Testing

Breath testing is a non-invasive test that is used fairly frequently as a way to diagnose or rule out SIBO. The test works by testing for the presence of hydrogen or methane in the breath at specific intervals after a person drinks a liquid containing a sugar solution, such as glucose or lactulose.

The presence of hydrogen in the breath prior to the 90-minute mark is thought to indicate that bacteria are present in the small intestine as they are interacting with the consumed sugar and releasing hydrogen or methane, which is then excreted through the breath. This cut-off time period is based on the fact that it typically takes two hours for an ingested sugar to reach the gut bacteria that are present within the large intestine, which is where such colonies are supposed to be.

Despite its wide use, concerns about the validity of breath tests for SIBO have been raised. One of the biggest concerns is the fact that the test yields too many false-positive results, particularly for people who have a rapid transit time of food through the digestive system, or false-negative results, most likely in people who have gastroparesis (slow emptying of the stomach).

In addition, there is no consensus on the best protocols for performing the test, nor is there a consensus on exactly what amounts of gas present in the breath constitutes a positive test result. Nevertheless, the simplicity and safety of the test are the primary reasons why this is the most popular way to test for SIBO.


  • Non-invasive

  • Easy to do

  • Safe


  • Many false positives and false negatives

  • No agreed-upon protocol

  • No agreement on cutoff for postive result

  • Testing requires proper preparation, fasting for 12 hours, and your presence for two to three hours

How to Prep for a SIBO Breath Test

First of all, you will want to choose a testing center that tests for both the presence of hydrogen and methane. Once you have done so, your doctor or the testing center itself will provide you with specific instructions on to how they want you to be prepared for the test. It is important that you follow their directions carefully to optimize the accuracy of the results. Here are some guidelines that are likely to be recommended to you:

  • One month before: Do not use any colon cleansing products (such as that used prior to a colonoscopy).
  • Two weeks before: Do not take any antibiotics or probiotics.
  • One week before: Do not use any laxatives, fiber supplements, or stool softeners.
  • 48 hours before: Avoid high carbohydrate meals and snacks, particularly whole grain bread or pasta. You can eat broiled fish or chicken, white bread or rice, potatoes, coffee, and tea. If you are taking a medication for GERD, discuss whether or not you should continue to take the medicine in the days leading up to the test. Typically, it is recommended that you discontinue the use of any prokinetic medications, but that you can continue with a PPI medication.
  • 12 hours before: Do not eat or drink anything. This includes gum and candy. If you are a smoker, do not smoke. Do not exercise, as exercise can throw off test results.

What to Expect When Undergoing the SIBO Breath Test

When the test starts, you may be asked to rinse your mouth with mouthwash to clear the area of any bacteria that may be present. You will then be asked to give a baseline breath sample, typically by blowing up a balloon. You will then be asked to drink a small amount of liquid containing either glucose or lactulose.

Every 15 minutes, you will be asked to provide another breath sample by blowing up a balloon. If the sample liquid contains glucose, you can expect the test to last for two hours. If the sample liquid is lactulose, you can expect the test to last for three hours.

Jejunal Aspiration

More invasive, but considered more accurate for diagnosing SIBO than the breath test, is a test called "jejunal aspiration." This procedure takes place during an upper endoscopy procedure and requires that a sample of fluid be taken from the middle section of your small intestine. The sample is then cultured and evaluated for the presence of bacteria.

Jejunal aspiration is not generally used. Its downsides are that it is costly, time-consuming, and while generally considered safe, still carries more risks than a breath test. This procedure also has its limitations in terms of accurately identifying the presence of SIBO.

A false negative may happen because the bacterial overgrowth is present in an area different from the one in which the sample was taken (for example, further along in the small intestine). Other reasons for a false-negative test result include a sample that is not large enough or that the culture used was one in which certain bacteria do not grow.

A false positive may occur if the sample was tainted due to bacteria present in the mouth, on the instruments used or through poor handling of the sample. And in regular clinical practice as opposed to research studies, physicians may be more likely to take the sample from the duodenum, the first part of the small intestine, as opposed to the jejunum. Despite all of these limitations, many researchers consider jejunal aspiration as the "gold standard" for SIBO testing.

How to Prep for a Jejunal Aspiration

Your doctor or the testing center will give you instructions on what to do to prepare for the aspiration procedure. Most likely those instructions will be similar to the instructions for the breath test. The only potential difference is if you have gastroparesis. In that case, you may be recommended to follow a liquid diet for three days prior to the test.

What to Expect When Undergoing a Jejunal Aspiration

The test will take place either at your doctor's office or at a testing facility. To start the procedure, monitors may be placed on your body so that your doctor can keep an eye on your breathing, heart rate, and blood pressure. An IV will most likely be started and you will receive mild sedation that will relax you but 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 will not be able to talk, but you will still be able to breathe. Your doctor will then take a sample of fluid from your small intestine using an aspiration catheter.

Once the procedure is complete, the tube will be removed from your throat. After that, you may rest for a while to allow the anesthesia to wear off. It is important to know that because the procedure requires sedation, you will not be allowed to drive yourself home following the test.

For the rest of the day, you should keep your activity to a minimum. Some people experience mild side effects such as gassiness, bloating, cramping or soreness in the throat area. If you experience any severe, unusual or worrisome symptoms (such as vomiting or coughing up blood), you should contact your doctor immediately.

Medication Trial

A fairly common way for doctors to assess the presence of SIBO is through the use of a trial of SIBO medication. Quick symptom relief would therefore suggest that SIBO was present.

The most commonly used medication for SIBO is Xifaxan, which is an antibiotic. Xifaxan is different from most of the antibiotics that you are familiar with as it is not absorbed into the body through your stomach. Instead, it acts locally on any bacteria that might be in your small intestine.

Although as of yet there are no standards for dosing amounts and duration, doctors might choose to follow the FDA guidelines for the use of Xifaxan for the treatment of diarrhea predominant IBS (IBS-D). These guidelines recommend that the medication be taken for a two-week period, and then repeated for another one or two weeks.

As with the other two approaches, there are limitations with this "therapeutic trial" approach. For one, as you can see, there are no guidelines as to how the antibiotics should be prescribed. There are also no guidelines as to what is considered a good response to the medication. All of this uncertainty means that you might be taking too much or too little of the medication.

The Future of SIBO Testing

Researchers are working at a better understanding of SIBO itself, as well as how to improve the validity of diagnostic testing methods. It is hoped that in the future, doctors will be able to accurately identify SIBO's presence, including specifying which types of bacteria are populating the small intestine of each individual and contributing to their symptoms.

Was this page helpful?

Article Sources