A Functional Medicine SIBO Protocol: Testing and Treatment

Imagine a scenario where a significant portion of those suffering from the frustrating and often debilitating symptoms of irritable bowel syndrome (IBS) could find a curative solution. This intriguing possibility lies in small intestinal bacterial overgrowth (SIBO), a condition increasingly recognized as a common underlying cause of IBS. 

By diving into the complexities of SIBO, medical practitioners and patients can discover a pathway to effective treatment and relief from chronic gastrointestinal distress.

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What Is Small Intestinal Bacterial Overgrowth (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 IBS symptoms. 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.

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 (6). H2-dominant SIBO is common in patients with (IBS-D) (48).
• 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). (41, 48)
• 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 Signs & 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
• Diarrhea (41)

Other gastrointestinal symptoms may include: 

• Heartburn
• Reflux
• Nausea
• Burping
• Constipation
• Fatty stools
• Food sensitivities (31, 41)

Leaky gut secondary to SIBO may cause 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. (41)

Root Causes of 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 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 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 digestive enzyme insufficiencies. (31, 45)

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. (31, 45)

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. (31, 45)

How to Diagnose 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.

Step 1: 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 after drinking a glucose- or lactulose-containing solution can be measured in the breath to diagnose SIBO and its various subtypes. 

SIBO can be diagnosed when any of the criteria are met: 

• Hydrogen-Dominant SIBO: H2 levels rise at least 20 ppm from baseline within the first 90 minutes of the test
• IMO: CH4 measures 10 ppm or above at any time during the test
• Hydrogen Sulfide-Dominant SIBO: H2S levels reach at least 3 ppm at any time during the test

Any one of these three breath tests can diagnose IMO: 

• SIBO - 3 Hour by Genova Diagnostics
• SIBO/IMO Lactulose Breath Test by Commonwealth Diagnostics International, Inc.
• trio-smart SIBO Breath Test by Gemelli Biotech

Step 2: Tests to Investigate the Root Cause of SIBO

A frequent, and reasonable, question asked among people with SIBO is, "How did I get it?" The following labs can help answer this question:

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. The ibs-smart panel by Gemelli Biotech measures both of these antibodies.

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.

• Comprehensive Thyroid Assessment by Genova Diagnostics
• Comprehensive Thyroid Panel w/ Antibodies by Precision Point

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 measurement of blood sugar used as a diagnostic marker for diabetes.

Cortisol Testing

Salivary cortisol testing can identify maladaptive stress responses by qualifying and quantifying cortisol secretion patterns. Cortisol imbalances caused by chronic stress can negatively influence gastrointestinal function.

• Adrenal Stress Profile by ZRT Laboratory
• Salivary Cortisol x 4 by Access Med Labs
• Adrenal Stress Panel by Ayumetrix

Imaging

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.

Step 3: Tests to Customize SIBO Treatment Plans

Additional tests can be considered to help individualize treatment plans. These tests may not be indicated for every individual but are commonly recommended by providers during a comprehensive gastrointestinal evaluation.

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. Alternatively, consequences of SIBO that can be screened for by stool analysis include malabsorption and leaky gut.  

These are popular comprehensive stool tests ordered through Rupa Health:

• GI-MAP + Zonulin by Diagnostic Solutions
• GI360 by Doctor's Data
• GI Effects Comprehensive Profile - 3 day by Genova Diagnostics

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.

Consider ordering one of the following tests to screen for nutritional deficiencies:

• NutrEval FMV by Genova Diagnostics
• Cellular Micronutrient Assay by Cell Science Systems
• Micronutrient Test from SpectraCell Laboratories 

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Treatment Plan for SIBO

This article will outline basic guidelines for treating patients with H2- and H2S-SIBO subtypes. A treatment protocol specific to IMO can be found in this article.

Step 1: Antimicrobial Therapy

Here's Why This Is Important:

The primary SIBO treatment goal is eradicating bacterial overgrowth to directly eliminate the cause of gastrointestinal symptoms.

How Do You Do This?

The American College of Gastroenterology recommends using prescription antibiotics to treat symptomatic patients with SIBO. Rifaxmin (Xifaxan) is the first-line and preferred nonabsorbable antibiotic for treating both the H2-and H2S-dominant SIBO subtypes. However, other antibiotics that have been studied in clinical trials for treating SIBO include amoxicillin-clavulanic acid, ciprofloxacin, doxycycline, metronidazole, neomycin, norfloxacin, tetracycline, and trimethoprim-sulfamethoxazole. Antibiotics are generally dosed for two weeks at a time; however, multiple courses may be required for complete SIBO eradication. (41) 

While research is limited, evidence suggests that adding bismuth subsalicylate (524 mg four times daily) to rifaximin therapy can expedite SIBO eradication for those with H2S-SIBO.

Herbal antimicrobials are proven to be equally effective as rifaximin in treating SIBO. 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 benefits and can be more expensive for the patient. As with prescription antibiotics, multiple courses of herbal antibiotics may be required for complete SIBO eradication.

The following herbs are most commonly utilized to treat SIBO:

• Berberine: 1,500-4,500 mg daily, split into three doses
• Oregano: 150-300 mg daily, divided between 2-3 doses
• Neem: 600 mg three times daily 

Combination herbal formulas can be an alternative to dosing single herbs together. The following botanical formulas are backed by evidence to eradicate SIBO:

• FC Cidal™ and Dysbiocide® by Biotics Research: 2 capsules of each twice daily (1)
• Candibactin-AR® and Candibactin-BR® by Metagenics: 2 capsules of each twice daily (1) 

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. Elemental formulas can be made at home or purchased commercially. Because elemental formulas are high in sugar, this may not be an appropriate option for patients with diabetes or small intestinal fungal overgrowth (SIFO). (18)

Step 2: Palliate Symptoms

Here's Why This Is Important:

The second goal of SIBO treatment is to alleviate symptoms, which can negatively impact the quality of life of those affected by SIBO. 

How Do You Do This?

Fermentable carbohydrates draw fluid into the bowels and are rapidly fermented by intestinal bacteria. This increased fluid and gas can aggravate symptoms during or after meals. 

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 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. (18)

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 3-4 hours.

In addition, a prokinetic agent can be added to either herbal or pharmaceutical antimicrobial therapy to support intestinal motility. Prokinetics can assist in relieving gas and bloating symptoms. Ginger, for example, is a popular natural prokinetic that has been shown to stimulate gastric emptying when administered to patients in a dose of 1.2 grams.

Step 3: Prevention

Why Is This Important?

Approximately 45% of patients experience recurrent SIBO after completing antibiotic therapy. Treating SIBO's underlying cause will help prevent recurrence.

How Do You Do This?

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 treating the various conditions that can predispose patients to SIBO.

The Risks of Untreated SIBO

One of the primary risks of untreated SIBO is malabsorption, which arises from the competition between the bacteria and the host for nutrients. Malabsorption can result in anemia, bone density loss, and neurological issues due to the deficiency of critical nutrients.

Chronic diarrhea can lead to electrolyte imbalances, dehydration, and weight loss. 

In severe cases, the bacterial overgrowth can produce toxins that damage the liver, leading to non-alcoholic fatty liver disease (NAFLD).

SIBO Case Study

To learn more about successfully treating SIBO, read this case study: 

How Amy Beat Chronic IBS After Suffering For 15 Years

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Key Takeaways:

• It's becoming clear that accurate diagnosis and effective treatment strategies hold immense promise for transforming outcomes for patients with chronic digestive symptoms and SIBO.
• By leveraging advanced diagnostic tools and tailored therapeutic approaches, healthcare practitioners can move beyond merely managing symptoms to addressing the root cause of chronic gastrointestinal discomfort.