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Understanding SIBO and the Role of Breath Testing

Small Intestinal Bacterial Overgrowth (SIBO) is a common yet underdiagnosed cause of bloating, gas, diarrhea, constipation, and malabsorption. SIBO occurs when bacteria overgrow in the small intestine, leading to fermentation, inflammation, and digestive dysfunction.

The SIBO breath test is the gold standard for diagnosing this condition. Functional medicine practitioners use this test to assess bacterial overgrowth, methane and hydrogen production, and underlying causes of gut dysbiosis, allowing for targeted, natural treatment strategies.

What is the SIBO Breath Test?

The SIBO breath test measures hydrogen (H2), methane (CH4), and hydrogen sulfide (H2S) gases produced by bacteria fermenting carbohydrates in the small intestine.

Patients drink a lactulose or glucose solution, and exhaled gases are measured over 2-3 hours to determine whether bacterial overgrowth is present.

Types of SIBO Detected by the Breath Test:

• Hydrogen-Dominant SIBO – Often linked to diarrhea (IBS-D)
• Methane-Dominant SIBO (IMO – Intestinal Methanogen Overgrowth) – Associated with constipation (IBS-C)
• Hydrogen Sulfide SIBO – Causes sulfur-smelling gas, diarrhea, and inflammation

A functional medicine approach to SIBO treatment considers the root causes of bacterial overgrowth, including low stomach acid, poor motility, food sensitivities, gut infections, and immune dysfunction.

Symptoms of SIBO

SIBO symptoms vary depending on the type of overgrowth, but common symptoms include:

Digestive Symptoms

• Chronic bloating and gas (worse after eating fiber, sugar, or starches)
• Abdominal discomfort or pain
• Diarrhea (IBS-D), constipation (IBS-C), or mixed bowel habits
• Reflux, burping, and nausea
• Fat malabsorption and floating stools

Systemic Symptoms

• Fatigue, brain fog, and mood changes (due to gut-brain axis dysfunction)
• Nutrient deficiencies (B12, iron, magnesium, zinc)
• Unexplained weight loss or difficulty gaining weight
• Joint pain, skin rashes, rosacea, or eczema
• Food intolerances (gluten, dairy, histamines, FODMAPs)

Functional Medicine Testing for SIBO and Gut Health

To confirm SIBO and identify underlying causes, functional medicine practitioners use comprehensive gut health assessments.

1. SIBO Breath Test (Lactulose or Glucose Test)

• Measures hydrogen (H2), methane (CH4), and hydrogen sulfide (H2S) levels
• Determines bacterial fermentation patterns in the small intestine
• Identifies which type of SIBO is present (hydrogen, methane, or hydrogen sulfide)

2. Comprehensive Stool Analysis (GI-MAP, PCR Testing)

• Detects dysbiosis, parasites, yeast overgrowth, and gut inflammation
• Assesses levels of beneficial and pathogenic bacteria
• Identifies enzyme deficiencies and malabsorption markers

3. Organic Acids Test (OAT)

• Evaluates bacterial and fungal overgrowth markers
• Identifies neurotransmitter imbalances and mitochondrial function

4. Leaky Gut & Zonulin Testing

• Assesses intestinal permeability (leaky gut syndrome)
• Helps identify inflammation and immune system dysfunction

5. Food Sensitivity & Histamine Intolerance Testing

• Determines if food intolerances are contributing to gut symptoms
• Assesses for gluten, dairy, FODMAPs, and histamine sensitivity

Functional Medicine Approach to Treating SIBO

A functional medicine strategy for SIBO involves a multi-phase approach:

1. Starve & Reduce Bacteria (Dietary Interventions)

• Low-FODMAP diet – Reduces fermentable carbohydrates that feed bacteria
• Specific Carbohydrate Diet (SCD) or Elemental Diet – Used for severe cases
• Reduce sugar, refined carbs, and processed foods

2. Herbal or Pharmaceutical Antimicrobials

• Berberine – Targets hydrogen-producing bacteria
• Allicin (Garlic Extract) – Effective against methane-producing archaea
• Oregano Oil & Neem – Broad-spectrum antimicrobials
• Atrantil – Targets methane SIBO (IMO)
• Xifaxan (Rifaximin) – FDA-approved antibiotic for hydrogen SIBO
• Neomycin or Metronidazole – Used alongside rifaximin for methane SIBO

3. Support Gut Motility & Prevent Relapse

• Prokinetics (Ginger, 5-HTP, MotilPro, Prucalopride) – Stimulates migrating motor complex (MMC)
• Magnesium Citrate & Aloe Vera – Natural motility enhancers
• Acupuncture & Vagus Nerve Stimulation – Improves gut-brain signaling

4. Repair Gut Lining & Reduce Inflammation

• L-Glutamine & Collagen – Repairs intestinal barrier
• Zinc Carnosine & Aloe Vera – Reduces gut inflammation
• Quercetin & Curcumin – Anti-inflammatory support

5. Restore the Microbiome & Optimize Digestion

• Spore-based probiotics (Bacillus coagulans, Akkermansia muciniphila) – Recolonizes the gut after treatment
• Digestive Enzymes & Betaine HCl – Supports digestion and prevents bacterial overgrowth
• Prebiotic fibers (inulin, resistant starch, PHGG) – Helps rebalance microbiome (used cautiously in SIBO patients)

Preventing SIBO Relapse: Long-Term Gut Health Strategies

SIBO often returns if the root cause is not addressed. Functional medicine practitioners focus on long-term gut health maintenance:

• Address underlying motility disorders (e.g., vagus nerve dysfunction, low stomach acid)
• Incorporate prokinetics (ginger, 5-HTP) to maintain healthy MMC function
• Follow a diverse, fiber-rich diet to prevent microbiome imbalances
• Minimize stress and optimize sleep for proper gut-brain communication

Who Should Get a SIBO Breath Test?

If you experience any of the following, a SIBO breath test may help uncover the cause:

• Chronic bloating and gas (especially after eating fiber or carbs)
• Constipation, diarrhea, or alternating bowel habits
• Acid reflux, nausea, and burping
• Unexplained fatigue, brain fog, or mood swings
• Skin issues (eczema, rosacea, acne)
• Food intolerances and difficulty digesting starches
• Persistent IBS symptoms that don’t improve with standard treatments

Final Thoughts: Why the SIBO Breath Test is Essential for Gut Health

SIBO is one of the most overlooked causes of digestive distress, but with the right testing and treatment, it can be successfully managed and prevented. A functional medicine approach provides a personalized gut healing plan using advanced testing, natural therapies, and dietary interventions