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A Functional Medicine SIBO Protocol: Testing and Treatment

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A Functional Medicine SIBO Protocol: Testing and Treatment

Small intestinal bacterial overgrowth (SIBO) is characterized by excessive bacterial growth within the small intestine. It is a common disorder, especially amongst the IBS population, and can cause significant disruptions in digestive function and quality of life. Therefore, diagnosing SIBO is important in the field of gastroenterology but, unfortunately, is commonly overlooked by allopathic medical doctors. Functional medicine doctors are better trained to diagnose and effectively treat SIBO in patients with digestive and extraintestinal manifestations of this bacterial imbalance.

This article will discuss the etiology, pathogenesis, and clinical manifestations of the three subtypes of SIBO and continue to discuss a functional medicine treatment protocol specific to the hydrogen and hydrogen sulfide SIBO subtypes. A future article will discuss a treatment protocol specific to intestinal methanogen overgrowth, the third subtype of SIBO.


What is SIBO?

Small intestinal bacterial overgrowth, or SIBO, is what the name implies - an overgrowth of bacteria within the small intestine. It is a prevalent gastrointestinal disorder, affecting at least 39 million people, and a commonly overlooked cause of irritable bowel syndrome (IBS)-like digestive symptoms, including abdominal pain, abnormal bowel movements, and bloating. The small intestine should house have a relatively small concentration of bacteria, but when levels increase, bacterial fermentation of dietary carbohydrates produces excess gas and causes symptoms.

What Types of SIBO Are There?

There are three distinct subtypes of SIBO, distinguished by the gaseous metabolic byproducts produced by the bacteria in the intestines.

Hydrogen (H2)-dominant SIBO is the overgrowth of bacteria in the small intestine diagnosed by elevated hydrogen gas levels on the SIBO breath test. Overgrowth of Streptococcus, E. coli, Staphylococcus, Micrococcus, Klebsiella, Bacteroides, and Peptostreptococcus are strongly associated with H2-dominant SIBO (1). H2-dominant SIBO is strongly associated with IBS-diarrhea (IBS-D) (2).

Intestinal methanogen overgrowth (IMO), previously called methane (CH4) dominant-SIBO, is the overgrowth of methanogens in the intestines. Methanogens, predominantly Methanobrevibacter smithii, are archaea (not bacteria) that can overgrow and overproduce methane gas in the colon and small intestine. As such, IMO has been proposed as a new term to describe CH4-positive breath tests. In contrast to SIBO, IMO is more strongly correlated with IBS-constipation (IBS-C). (2, 3)

The most recently discovered SIBO subtype is hydrogen sulfide (H2S)-dominant SIBO, characterized by excess bacterial production of H2S gas. Hydrogen sulfide-producing bacteria associated with SIBO include Escherichia, Klebsiella, Proteus, and Desulfovibrio. Research suggests that diarrheal presentations are more common in patients with H2S-dominant SIBO.

SIBO Symptoms

SIBO symptoms arise from bacterial fermentation within the small intestine, intestinal immune activation and inflammation, increased intestinal permeability, and poor digestion and absorption of nutrients. The most common symptoms of SIBO include abdominal pain, gas, flatulence, bloating, abdominal distension, and diarrhea. Other gastrointestinal symptoms may include heartburn, reflux, nausea, burping, constipation, fatty stools, and increasing food sensitivities. (3, 4)

Leaky gut caused by SIBO may be responsible for symptoms outside the digestive tract, including fatigue, brain fog, headaches, changes in mood, skin issues, and joint pain.

Additionally, because SIBO can disrupt healthy digestion and absorption, it's not uncommon for nutrient deficiencies to manifest. Vitamin B12, vitamin D, and iron deficiencies are most commonly measured on blood tests. (3)

What Causes SIBO?

SIBO can result from various medications, medical conditions, and lifestyle habits. Simply put, SIBO most often results from reduced intestinal immunity, motility, and compartmentalization.

Stomach acid and other digestive enzymes act as part of the body's first line of defense against infection by killing bacteria passing through the digestive tract. Bacteria can overgrow within the upper digestive tract when there are deficiencies in stomach acid, pancreatic enzymes, and/or bile. Chronic stress, use of proton pump inhibitors or other acid-blocking medications, H. pylori infection, and cholecystectomy (gallbladder removal surgery) are possible reasons for suboptimal digestive enzymes. (4, 5)

The migrating motor complex (MMC) is a reflexive wave of small intestinal smooth muscle contractions (peristalsis) that occurs in a fasting state. A diminished MMC and slowed intestinal motility impair the downward movement of bacteria through the small intestine into the colon. Frequent eating, stress, hypothyroidism, diabetes, gastroparesis, and food poisoning can negatively impact intestinal motility. (4, 5)

Intestinal and abdominal structural abnormalities can impair intestinal motility and weaken the sphincters that compartmentalize the small and large intestines. An incompetent ileocecal valve, abdominal surgeries and resulting scar tissue, and fistulas may contribute to the development of SIBO. (4, 5)

Functional Medicine Labs to Test for Diagnosis of SIBO

SIBO can be diagnosed through a small intestinal aspirate culture or breath test. Due to the invasive nature and cost of small intestinal culture, the SIBO breath test is most commonly utilized in the clinical setting to diagnose SIBO.

SIBO Breath Test

The SIBO breath test can be performed at home by the patient after completing a one-day preparatory diet. Bacterial fermentation gas products exhaled through the lungs can be measured in the breath to diagnose SIBO and its various subtypes. High H2, CH4, and H2S levels are diagnostic for H2-dominant SIBO, IMO, and H2S SIBO, respectively. Most available SIBO breath tests only measure H2 and CH4 gas levels, except for the trio-smart, which measures all three gas types.

Vinculin & CdtB Antibodies

Food poisoning increases the risk for IBS by four times. Positive vinculin and CdtB antibodies confirm a diagnosis of post-infectious IBS, which is indicative of intestinal motility dysfunction and increased incidence of SIBO. In conjunction with a positive SIBO breath test, positive antibodies confirm food poisoning as the cause of SIBO.

Functional Medicine Labs to Test To Help Personalize SIBO Treatment

A frequent, and reasonable, question asked among people with SIBO is, "How did I get it?" Functional medicine labs can help answer this question and guide personalized treatment plan recommendations.

Comprehensive Stool Test

Comprehensive stool tests measure fecal biomarkers that can provide insight into the underlying causes and consequences of SIBO. Digestive enzyme deficiencies, intestinal inflammation, and large intestinal dysbiotic patterns can be identified as potential contributors to SIBO pathogenesis through a stool analysis. Alternatively, consequences of SIBO that can be screened for by stool analysis include malabsorption and leaky gut.  

Cortisol Testing

Salivary cortisol testing can identify maladaptive stress responses by qualifying and quantifying cortisol secretion patterns. Functional cortisol testing can help identify chronic stress and cortisol imbalances that negatively influence gut function.

Micronutrient Testing

Nutrient deficiencies caused by SIBO can exacerbate extraintestinal symptoms and impair gut healing. Diagnosing suboptimal and deficient micronutrient levels, like iron, vitamin D, and zinc, with a comprehensive nutritional assessment helps providers to recommend specific dietary and supplemental recommendations.

Thyroid Panel

Hypothyroidism impairs digestive enzyme secretions and intestinal motility, perpetuates intestinal and systemic inflammation, and exacerbates symptoms like fatigue and constipation. A complete thyroid panel measures hormones and immune proteins involved in thyroid hormone production to screen for suboptimal thyroid function and overt hypothyroidism.

Hemoglobin A1c (HbA1c)

Diabetes-related nerve damage to the intestines causes gastroparesis (slowed stomach emptying) and impaired intestinal motility. HbA1c is a three-month average blood sugar that is diagnostic for diabetes.


Some patients may need imaging to confirm the diagnosis of inflammatory bowel disorders, structural abnormalities, and MMC deficiencies. Imaging options include antroduodenal manometry, endoscopy, colonoscopy, and barium follow-through.

Functional Medicine Treatment Protocol for SIBO

This article will outline basic antimicrobial guidelines to follow for patients with H2 and H2S SIBO subtypes. Given the complexity of SIBO pathogenesis, this article cannot outline protocols to address every potential root cause. Remember this is a crucial aspect of SIBO treatment to prevent recurrence, and interventions should be customized to your patient's needs and history. The Rupa Health Magazine has a lot of information on functional medicine approaches to conditions that can predispose patients to SIBO.

Therapeutic Diet and Nutrition Considerations for SIBO

Modifying the diet to limit fermentable carbohydrates can be helpful in providing symptom relief as SIBO is being treated. It is important to note that dietary modifications are not required for SIBO eradication, and elimination diets should especially be approached carefully (or avoided altogether) in patients with a history of eating disorders or an already limited diet.

Elemental Diet

The elemental diet (ED), a formula of predigested nutrients, is the only current diet with data supporting its ability to eradicate SIBO by evidence of a negative SIBO breath test after 14 days. This approach seeks to starve the bacteria, but feed the person, by replacing all meals with an elemental formula for two weeks. It is highly effective, especially for severe cases of SIBO, resulting in 80% eradication rates after two weeks of treatment. Common commercial elemental formulas include Elemental Heal Whey Free, Physicians' Elemental Diet, and Vivonex Plus. (6)

Because elemental formulas are high in sugar, this may not be an appropriate option for patients with diabetes. Additionally, fungal overgrowth is a common side effect, so antifungal prophylaxis, typically with prescription nystatin, is recommended.

Palliative Diets

Diets that reduce the intake of fermentable carbohydrates can effectively provide SIBO symptom relief. The proper diet for your patient depends on the one that fits their personal preferences and lifestyle and will be sustainable. The low FODMAP, Specific Carbohydrate (SCD), Bi-Phasic, GAPS, and Cedars-Sinai diets are all clinically effective options. Strict elimination diets should be followed for as little time as needed, with the goal of reintroducing variety back into the diet as SIBO and leaky gut are treated. (6)

Meal spacing can encourage a healthy MMC and provide symptomatic relief, regardless of other dietary modifications implemented. Patients should be advised to space meals during the day by 4-5 hours, eat their last meal two hours before bed, and fast overnight for 10-12 hours.

Prescription Antibiotic Protocol for SIBO

Rifaximin (Xifaxan) is the first-line and preferred prescription antibiotic for treating H2 and H2S SIBO. A course of prescription antibiotic treatment is two weeks; however, multiple courses may be required for complete SIBO eradication.

Dose: 550 mg three times daily

Duration: 2 weeks

Research is limited, but suggests that adding bismuth subsalicylate to rifaximin can expedite SIBO eradication for those with the H2S subtype.

Dose: 524 mg four times daily

Duration: 2 weeks

Herbal Antibiotic Protocol for SIBO

Herbal therapy has been shown to be equally as effective to Rifaximin for the treatment of small intestinal bacterial overgrowth.

An herbal antibiotic protocol for treating SIBO involves dosing two herbs or formulas together for six weeks before reassessment. Dosing more than two single herbs simultaneously does not usually provide additional benefit, and can be more expensive, for the patient. As with prescription antibiotics, multiple courses of herbal antibiotics may be required for complete SIBO eradication.

Functional Medicine Practitioners will commonly use herbal antimicrobials (antibiotics) alongside a low FODMAP diet for 6 weeks. Patients should be warned that they will have bacteria and possible candida die off (if present) and may feel worse before feeling better up to 3-4 weeks during treatment.


Berberine is a broad-spectrum antimicrobial, effective against bacteria, fungi, viruses, and parasites (7). Berberine can also attenuate intestinal permeability by exerting antioxidant, anti-inflammatory, and mucosal healing effects (8).

Dose: 1,500-5,000mg daily, split into three doses

Duration: 6 weeks


Oregano has shown many therapeutic properties: antimicrobial, antiviral, antifungal, antioxidant, anti-inflammatory, and antispasmodic (9). While being broadly antimicrobial, research does suggest that oregano selectively targets pathogenic bacteria while leaving Lactobacilli and Bifidobacterium of the healthy microbiome alone (10).

Dose: 150-300 mg daily, split between 2-3 doses

Duration: 6 weeks


Neem is well recognized for its antimicrobial effects against bacteria, malaria, viruses, and fungi (11). While there are safety concerns with neem oil, especially in children, neem leaf is safe.

Dose: 900-1,800 mg daily, split into three doses

Duration: 6 weeks

FC-Cidal & Dysbiocide

Combination herbal formulas can be an alternative to dosing single herbs together. FC Cidal™ and Dysbiocide® by Biotics Research is a combination of formulas backed by evidence to eradicate SIBO. (12)

Dose: 2 capsules of each twice daily

Duration: 6 weeks


Candibactin-AR® and Candibactin-BR® by Metagenics is another combination of herbal formulas proven effective in eradicating SIBO when administered daily for four weeks. (12, 13)

Dose: 2 capsules of each twice daily

Duration: 6 weeks

Additional Supplements to Consider During SIBO Treatment

A prokinetic is an agent that promotes small intestinal motility. Prokinetic therapy during and after antimicrobial treatment supports the MMC and downward movement of bacteria out of the small intestine. Prokinetics can encourage SIBO eradication and prevent quick relapse after antimicrobials have been discontinued. Motility Activator by Integrative Therapeutics is a blend of ginger and artichoke commonly recommended by functional medicine providers to support intestinal motility.

Dose: 2-3 capsules before bed

Duration: start during or immediately after antimicrobial therapy, and continue for up to 4 months after SIBO eradication

When to Retest Labs

Repeating the SIBO breath test is unnecessary after a course of antimicrobial therapy but can help monitor treatment progress and confirm SIBO eradication. A patient can repeat the SIBO breath test after completing a course of antimicrobial therapy. Unlike the baseline SIBO breath test, the patient does not need to wait two weeks after completing prescription or herbal antibiotics to repeat the SIBO breath test; repeating the test as soon as possible will give the most accurate results as to how effective the treatment was.

Alternatively, patients and their doctors can decide against retesting, a common preference given the cost and inconvenience of testing. If patients choose not to retest after completing a course of antibiotics, SIBO symptoms should be monitored instead to determine whether treatment should be continued or discontinued. SIBO treatment is considered to be successful when the patient reports an 80-90% improvement in SIBO symptoms.



Small intestinal bacterial overgrowth is a common digestive disorder characterized by bacterial overgrowth in the wrong place. It can cause significant symptoms related to and outside the digestive tract and health complications associated with the resulting leaky gut and malabsorption.

Successful treatment of SIBO relies upon correcting the imbalances predisposing an individual to bacterial overgrowth and antibiotic therapy. Treatment can be complex, and SIBO recurrence is common, because of the many factors that can contribute to SIBO development. Functional testing helps identify SIBO root causes so that measures can be implemented to prevent SIBO recurrence and support healthy gastrointestinal function.

Lab Tests in This Article

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2. Takakura, W., & Pimentel, M. (2020). Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome – An Update. Frontiers in Psychiatry, 11.

3. Pimentel, M., Saad, R.J., Long, M.D., et al. (2020). ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. The American Journal of Gastroenterology, 115(2), 165–178.

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

5. Sorathia, S.J., Chippa, V., & Rivas, J.M.(2022). Small Intestinal Bacterial Overgrowth. StatPearls Publishing.

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

7. Clinical Applications for Berberine. (2022). Natural Medicine Journal.

8. Habtemariam, S. (2016). Berberine and inflammatory bowel disease: A concise review. Pharmacological Research, 113, 592–599.

9. Oniga, I., Pușcaș, C., Silaghi-Dumitrescu, R., et al. (2018). Origanum vulgare ssp. vulgare: Chemical Composition and Biological Studies. Molecules, 23(8), 2077.

10. Si, W., Gong, J., Tsao, R., et al. (2006). Antimicrobial activity of essential oils and structurally related synthetic food additives towards selected pathogenic and beneficial gut bacteria. Journal of Applied Microbiology, 100(2), 296–305.

11. Jerobin, J., Makwana, P., Kumar, R.S.V., et al. (2015). Antibacterial activity of neem nanoemulsion and its toxicity assessment on human lymphocytes in vitro. International Journal of Nanomedicine, 77.

12. Achufusi, T.G., Kachroo, P., Zamora, E., et al. (2020). Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis, Prevention, and Treatment Methods. Cureus.

13. Chedid, V., Dhalla, S., Clarke, J., Roland, B. C., Dunbar, K. B., Koh, J. H. L., Justino, E., Tomakin, E., & Mullin, G. E. (2014). Herbal Therapy is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth. Global Advances in Health and Medicine, 3(3), 16–24.

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