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When To Order A SIBO Test For Your Patients

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When To Order A SIBO Test For Your Patients

Small intestinal bacterial overgrowth (SIBO) is a significant and often underdiagnosed challenge within the realm of gastrointestinal disorders. SIBO is estimated to affect over 80% of patients with irritable bowel syndrome alone. Given its prevalence and the overlapping nature of symptoms with other conditions, accurate diagnosis becomes paramount in providing effective patient care. SIBO testing plays a crucial role by enabling healthcare professionals to identify and quantify bacterial overgrowth, guiding them in making tailored treatment recommendations. Recognizing the importance of precise diagnostics in the complex landscape of gastrointestinal health, SIBO testing emerges as a valuable tool in enhancing the accuracy of diagnoses and, consequently, improving the overall quality of patient care.


What Is SIBO?

Small intestinal bacterial overgrowth, or SIBO, encompasses three subtypes of intestinal microbial overgrowth: hydrogen-dominant SIBO, hydrogen sulfide-dominant SIBO, and intestinal methanogen overgrowth (IMO). Simply stated, SIBO describes a condition in which bacteria and/or archaea (bacteria-like microorganisms) overgrow in the intestines. 

Normally, the small intestine contains a relatively low number of bacteria due to several factors (7):

  1. The sweeping action of the migrating motor complex (MMC), which helps to move bacteria through the digestive tract
  2. The stomach's acidic environment 
  3. The immune system
  4. Intestinal anatomy

SIBO can occur when a circumstance disrupts these innate defense mechanisms, contributing to low stomach acidity, small intestinal dysmotility, immune dysfunction, and/or structural problems within the intestines. Any or all of these can upset the healthy balance of the microbiota and create a breeding ground for bacteria and archaea. (7

Indications for SIBO Testing

How do you know when to test for SIBO? The most common indication for SIBO testing is the presence of gastrointestinal (GI) symptoms. SIBO is a form of dysbiosis, an imbalance in the gut microbiota, and a common cause of GI symptoms. Evidence suggests the most common SIBO symptoms, present in more than two-thirds of afflicted patients, are abdominal pain, bloating, gas, distension, flatulence, and diarrhea. These symptoms overlap with those of irritable bowel syndrome (IBS); studies have found that up to 84% of patients with IBS have SIBO, suggesting SIBO may be an underlying cause of this functional GI disorder.

Research also suggests a link between SIBO and celiac disease, an autoimmune disorder characterized by a damaging immune response to ingesting gluten, a protein found in wheat, barley, and rye, leading to inflammation and damage to the small intestine. Meta-analyses have calculated SIBO prevalence rates of 20.8% in celiac disease patients and have also noted improved GI symptoms when SIBO is treated. SIBO testing is indicated for all celiac patients, especially those who are non-responsive to a gluten-free diet.

SIBO is also associated with many other health conditions, either as a cause or an effect of a co-existing condition, including autoimmune arthritis, diabetes mellitus (types 1 and 2), interstitial cystitis, rosacea, and restless legs syndrome. Given the high prevalence rates of SIBO in these patient populations, SIBO screening is appropriate during a holistic and comprehensive evaluation. 

In more severe cases, SIBO can cause malabsorption, nutritional deficiencies (namely, vitamin B12, vitamin D, and iron), and anemia (23). Patients with persistent and unexplained steatorrhea (fatty stools), nutrient deficiencies, and anemia should be screened for SIBO.

How to Test for SIBO

Different types of SIBO tests can be used for diagnosis. Small bowel aspirate and culture is often considered the gold standard for SIBO diagnosis. In this procedure, a catheter is passed in the distal duodenum (the first portion of the small intestine) through an endoscope, and fluid is aspirated for culture. The North American Consensus considers a bacterial colony count of  ≥103 colony-forming units per milliliter (CFU/mL) in a duodenal aspirate as diagnostic of SIBO. (24

Small bowel aspiration is invasive, time-consuming, costly, and not without risk. Given this, breath testing is now widely used as a noninvasive and less expensive alternative SIBO testing method. SIBO breath tests indirectly test for SIBO by measuring breath hydrogen (H2), methane (CH4), and hydrogen sulfide (H2S) gases. The premise of the SIBO breath test is that human cells cannot produce these gases; therefore, detecting these gases in breath samples signifies their production through microbial fermentation of carbohydrates in the gut. (23

The patient performs the SIBO breath test at home. The test begins with a 1-2 day preparation diet, followed by an overnight fast. On the morning of test collection, the patient starts by collecting a baseline breath sample and drinking a water mixture containing either glucose or lactulose. The patient continues collecting breath samples for 2-3 hours at timed intervals. (5)  

Two types of breath tests may be used to diagnose SIBO: the lactulose and glucose breath tests. Unfortunately, there is no perfect breath test, and choosing the right SIBO test will depend on the patient's history and the ordering provider's preferences. Glucose is absorbed by the small intestine, meaning glucose breath tests cannot detect SIBO or IMO in the distal portions of the intestines. However, glucose breath tests produce fewer false positives than lactulose breath tests and are the preferred option for patients with a lactulose allergy. Because humans cannot digest or absorb lactulose, the advantage of the lactulose breath test is that it can diagnose SIBO and IMO in the distal portions of the small intestine, where it is most common. (4

Until recently, SIBO breath tests could only measure hydrogen and methane gas levels. Now, one test on the market can measure all three gas types associated with SIBO: the trio-smart SIBO Breath Test by Gemelli Biotech. Other SIBO breath tests available for order through Rupa Health include: 


Interpreting SIBO Test Results

Once you've ordered a SIBO breath test, the next step is understanding breath test readings to interpret the test results accurately.

A SIBO breath test report includes several key components:

  • Baseline Measurements: The initial breath sample collected before ingesting the test substrate to serve as a baseline for comparison
  • Substrate Ingestion: Details about the type of substrate (glucose or lactulose) ingested
  • Breath Sample Collection: Timing and frequency of breath sample collections during the testing period
  • Gas Concentrations: Measurement of hydrogen and methane (and hydrogen sulfide, if trio-smart is used) in each breath sample. This is presented in both graph and chart form.

According to the North American Consensus, a SIBO test is positive if one of the following criteria is met: 

  • Hydrogen-SIBO: H2 levels rise at least 20 ppm from baseline within the first 90 minutes of the test
  • IMO: CH4 level is at least 10 ppm at any time point during the test
  • Hydrogen Sulfide-SIBO: a cut-off value for H2S gas has not yet been validated; however, trio-smart will report a positive test if H2S is at least 3 ppm at any point during the test (3, 23

Notably, methane gas directly slows intestinal motility, causing constipation. In patients with constipation, a methane level as low as 3 ppm at any time during the test can be considered positive. (11, 24

The interpretation of breath tests with elevated baseline H2 greater than 20 ppm is unclear. A high baseline H2 that plummets over the next two hours indicates improper test preparation (i.e., nonadherence to preparation diet), and the test should be repeated to ensure accuracy. (24

For SIBO breath tests that do not directly measure H2S, results with no CH4 and a low fixed H2 – giving a "flatline" result pattern on a graphical representation – suggest hydrogen sulfide-SIBO. (24

Functional Medicine Perspective on SIBO

The functional medicine approach to SIBO emphasizes a comprehensive understanding of the interconnectedness of various bodily systems. SIBO is not an isolated condition but a manifestation of underlying imbalances in the GI system and beyond.

Functional medicine considers factors such as diet, lifestyle, stress, genetics, and environmental influences in assessing SIBO. It recognizes that the digestive system is intricately linked to other physiological processes, including immune function, hormonal balance, and detoxification pathways. Therefore, addressing SIBO from a functional medicine standpoint involves a holistic assessment of gut health and a personalized treatment approach to restore balance to the entire body.

Treatment strategies (discussed in more detail below) include a combination of dietary interventions, lifestyle modifications, targeted supplements, and antimicrobial agents to eradicate overgrowth and treat the underlying imbalances to prevent overgrowth recurrence once antimicrobial therapy has been completed.

How to Treat SIBO Naturally

SIBO eradication involves using antibiotics to kill the bacteria and methanogens overgrowing in the gut. Conventionally, this means using prescription antibiotics (typically some combination of rifaximin, metronidazole, and neomycin) for at least two weeks. The good news is that herbal antibiotic options are just as effective as their prescription counterparts for patients who do not respond to antibiotic therapy or prefer to avoid antibiotics altogether. Herbal protocols typically involve using a combination of two herbs at a time. Standard options include berberine, oregano, neem, and allicin. Commercial herbal formulas have also been used to eradicate SIBO successfully. (6

Diet is also commonly used adjunctively during SIBO eradication. Most diets advertised to treat SIBO haven't actually been proven to treat SIBO*. Instead, dietary strategies should focus on reducing the consumption of fermentable products to reduce gas production and symptom severity. The low-FODMAP, SIBO Bi-Phasic, Specific Carbohydrate, and GAPS diets are examples of diets that reduce fermentable carbohydrates to achieve these desired effects. Therapeutic dietary therapy may be continued for up to one-month post-antimicrobial therapy to assist in the repair of the small intestinal lining from damage caused by the SIBO. (

* The one exception to this is the elemental diet. This liquid hypoallergenic formula fulfills human caloric and nutritional needs while devoid of all nutrients required to sustain bacterial life. Preliminary data show that the elemental diet is 80-85% effective in normalizing SIBO breath tests and improving associated GI symptoms in patients with IBS. 

Approximately 45% of patients will have recurrent SIBO following cessation of antibiotic therapy. This supports the notion that SIBO is a symptom of an underlying disorder and the need for adjunctive treatment measures that correct anatomical variations, immunodeficiencies, digestive enzyme insufficiencies, and intestinal dysmotility that increase the risk of SIBO. Personalized SIBO treatment strategies may include, but are not limited to:

  • Visceral manipulation to encourage normal mobility of internal organs, connective tissues, and ligaments
  • Taper and discontinuation of medications known to increase SIBO risk, such as narcotics and gastric acid suppressants
  • Digestive enzymes to replace hydrochloric acid, bile, and pancreatic enzymes, which have natural antimicrobial properties
  • Stress management to address chronic stress, which can suppress digestive enzyme secretion and impair intestinal motility
  • Prokinetics, which promote upper GI motility by activating the MMC. A popular option is ginger, which has been shown to increase gastroduodenal motility during phase III of the MMC in fasting and postprandial (after eating) states.  

Monitoring and Follow-Up

Given high SIBO recurrence rates, follow-up care during and after SIBO treatment is important. Repeat SIBO breath tests aren't required, but they can help monitor SIBO treatment progress and confirm SIBO eradication. If you decide against repeat SIBO testing, treatment progress should be gauged by monitoring the patient's changes in symptoms. Desired primary clinical outcomes include improvements in bloating and bowel movement habits. Any other laboratory abnormalities, such as anemia, should also be monitored for improvement and resolution during treatment. 


When To Order A SIBO Test: Final Thoughts

SIBO testing is a convenient diagnostic tool for identifying and addressing the complexities of small intestinal bacterial overgrowth. Timely and appropriate testing is crucial in clinical practice to unveil potential underlying causes of gastrointestinal symptoms and guide healthcare providers in tailoring effective treatment plans. By understanding the unique bacterial landscape of the small intestine through SIBO testing, clinicians can make informed decisions, leading to more effective interventions and improved patient outcomes. 

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
Learn More

Lab Tests in This Article


1. Achufusi, T. G. O., Sharma, A., Zamora, E. A., et al. (2020). Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis, Prevention, and Treatment Methods. Cureus, 12(6).

2. Cloyd, J. (2023, March 1). How to Use The Elemental Diet in Clinic. Rupa Health.

3. Cloyd, J. (2023, March 10). How to Use the trio-smart Test from Gemelli Biotech in Clinic. Rupa Health.

4. Cloyd, J. (2023, March 14). How to Use the SIBO/IMO Breath Tests from Commonwealth Diagnostics in Clinic. Rupa Health.

5. Cloyd, J. (2023, March 14). SIBO Testing 101: A Complete Guide to The Top 3 SIBO Tests. Rupa Health.

6. Cloyd, J. (2023, March 30). An In-Depth Overview of the Three Types of SIBO: Hydrogen, Methane, Hydrogen Sulfide. Rupa Health.

7. Cloyd, J. (2023, April 3). 5 Health Conditions That Are Associated with Small Intestinal Bacterial Overgrowth (SIBO). Rupa Health.

8. Cloyd, J. (2023, April 26). Dietary Modifications for a Successful SIBO Treatment Plan. Rupa Health.

9. Cloyd, J. (2023, May 4). A Functional Medicine SIBO Protocol: Testing and Treatment. Rupa Health.

10. Cloyd, J. (2023, May 24). What are Digestive Enzymes: How to Test Your Patients Levels. Rupa Health.

11. Cloyd, J. (2023, June 13). A Functional Medicine Intestinal Methanogen Overgrowth Protocol (IMO): Testing, Nutrition, and Supplements. Rupa Health.

12. Cloyd, J. (2023, June 23). Individualizing The SIBO Bi-Phasic Meal Plan With Specialty Labs. Rupa Health.

13. Cloyd, J. (2023, June 26). 5 Functional Medicine Lab Tests That Can Be Run During the GAPS Diet Protocol to Customize Nutritional Needs for Your Patients. Rupa Health.

14. DeCesaris, L. (2022, June 6). What Is Gut Dysbiosis? 7 Signs To Watch For. Rupa Health.

15. DePorto, T. (2023, January 26). Using the Specific Carbohydrate Diet for IBD Symptom Relief. Rupa Health.

16. Greenan, S. (2021, November 2). Constant Burping Is A Sign Of This Harmful Bacterial Overgrowth. Rupa Health.

17. Greenan, S. (2021, November 5). A Functional Medicine Approach To IBS. Rupa Health.

18. Greenan, S. (2021, November 18). How To Do A Low FODMAP Elimination Diet. Rupa Health.

19. Losurdo, G., Marra, A., Shahini, E., et al. (2017). Small intestinal bacterial overgrowth and celiac disease: A systematic review with pooled-data analysis. Neurogastroenterology and Motility, 29(6).

20. Micklefield, G. H., Redeker, Y., Meister, V., et al. (1999). Effects of ginger on gastroduodenal motility. International Journal of Clinical Pharmacology and Therapeutics, 37(7), 341–346.

21. Pimentel, M., Chow, E. J., & Lin, H. C. (2003). Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome: a double-blind, randomized, placebo-controlled study. The American Journal of Gastroenterology, 98(2), 412–419.

22. Pimentel, M., Constantino, T., Kong, Y., et al. (2004). A 14-day elemental diet is highly effective in normalizing the lactulose breath test. Digestive Diseases and Sciences, 49(1), 73–77.

23. Pimentel, M., Saad, R. J., Long, M. D., et al. (2020). ACG Clinical Guideline. The American Journal of Gastroenterology, 115(2), 165–178.

24. Rezaie, A., Buresi, M., Lembo, A., et al. (2017). Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. The American Journal of Gastroenterology, 112(5), 775–784.

25. Shah, A., Thite, P., Hansen, T., et al. (2022). Links between celiac disease and small intestinal bacterial overgrowth: A systematic review and meta‐analysis. Journal of Gastroenterology and Hepatology, 37(10), 1844–1852.

26. SIBO (Small Intestinal Bacterial Overgrowth). (2021, September 19). Cleveland Clinic.

27. Sorathia, S. J., & Rivas, J. M. (2020). Small Intestinal Bacterial Overgrowth. PubMed; StatPearls Publishing.

28. Weinberg, J. L. (2022, February 28). An Integrative Medicine Approach to Celiac Disease. Rupa Health.

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