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

Have you or your healthcare provider 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 healthcare provider 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.

Doctor holding endoscope
Air Rabbit/Getty Images

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.

People who have celiac disease but continue to experience symptoms despite strict adherence to a gluten-free diet might also be tested.

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.

Concerns about the validity of SIBO breath tests have been raised despite its wide use. The test yields many false-positive results, particularly for people who have a rapid transit time of food through the digestive system, as well as 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

Before the Test

First, you will want to choose a testing center that tests for both the presence of hydrogen and methane. Once you have done so, your healthcare provider or the testing center itself will provide you with specific instructions on 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).
  • Four weeks before: Do not take any antibiotics or probiotics.
  • One week before: Do not use any laxatives, fiber supplements, or stool softeners.
  • Eating and drinking 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.
  • Medication restrictions 48 hours before: Discuss any medications for gastroesophageal reflux disease (GERD) with your healthcare provider to see if they should be discontinued. Typically, it is recommended you discontinue the use of any prokinetic medications, but 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.

During the 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.

It 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.

Jejunal aspiration 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.

In regular clinical practice as opposed to research studies, healthcare providers 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.

Before the Test

Your healthcare provider 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.

During the Test

The test will take place either at your healthcare provider'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 healthcare provider 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 healthcare provider immediately.

Medication Trial

A fairly common way for healthcare providers 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 (rifaximin), 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, healthcare providers 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, healthcare providers 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.

Frequently Asked Questions

  • How accurate is the breath test for small intestinal bacteria?

    Not very. 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, with the sensitivity and specificity of the tests ranging from 44% to 83%.

  • What does SIBO feel like?

    Symptoms of SIBO are similar to other gastrointestinal problems, including these common signs:

    • Abdominal pain
    • Abdominal distension (swelling)
    • Bloating
    • Diarrhea
    • Flatulence
  • Is a small intestine aspiration painful?

    You’re sedated and may be given a local anesthetic to numb the areas where the endoscope is inserted, so you shouldn’t feel any pain during the procedure. As the medication wears off, you may have cramping and soreness. If this is extremely painful or if you’re also coughing up blood, contact your healthcare provider.

Was this page helpful?
Article 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.
  1. Salem A, Roland BC. Small intestinal bacterial overgrowth (SIBO). J Gastroint Dig Syst. 2014;4:225. doi:10.4172/2161-069X.1000225

  2. Ghoshal UC, Shukla R, Ghoshal U. Small intestinal bacterial overgrowth and irritable bowel syndrome: a bridge between functional organic dichotomy. Gut Liver. 2017;11(2):196-208. doi:10.5009/gnl16126

  3. Grace E, Shaw C, Whelan K, Andreyev H. Review article: small intestinal bacterial overgrowth – prevalence, clinical features, current and developing diagnostic tests, and treatment. Aliment Pharmacol Ther. 2013;38(7):674-88.

  4. 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

  5. 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

  6. U.S. Food and Drug Information. FDA approved drugs: Xifaxan: labeling/package insert. December 18, 2017.

  7. Saad RJ, Chey WD. Breath testing for small intestinal bacterial overgrowth: maximizing test accuracy. Clinical Gastroenterology and Hepatology. 2014;12(12):1964-1972. doi:10.1016/j.cgh.2013.09.055

  8. Achufusi TGO, Sharma A, Zamora EA, Manocha D. Small intestinal bacterial overgrowth: comprehensive review of diagnosis, prevention, and treatment methods. Cureus. 2020;12(6). doi:10.7759%2Fcureus.8860

  9. Mount Sinai Hospital. Small Intestine Aspirate and Culture.

Additional Reading