SIBO: A Functional Medicine Approach to Small Intestinal Bacterial Overgrowth
Small Intestinal Bacterial Overgrowth (SIBO) is a condition where an excessive number of bacteria grow in the small intestine, leading to digestive discomfort, nutrient malabsorption, and systemic inflammation. While conventional treatments often rely on antibiotics, functional medicine takes a root-cause approach, addressing factors like gut motility, microbiome imbalances, and dietary triggers to achieve long-term relief.
In this article, we’ll explore what causes SIBO, its symptoms, and functional medicine strategies for testing, treatment, and long-term gut health.
What is SIBO?
SIBO occurs when bacteria that normally reside in the large intestine migrate to the small intestine, where they ferment carbohydrates and produce excess gas. This fermentation process leads to bloating, gas, and other digestive symptoms.
Types of SIBO:
Hydrogen SIBO: Produces excessive hydrogen gas, leading to diarrhea-predominant symptoms (SIBO-D).
Methane SIBO (IMO - Intestinal Methanogen Overgrowth): Produces methane gas, causing constipation-dominant symptoms (SIBO-C).
Hydrogen Sulfide SIBO: Produces hydrogen sulfide gas, leading to a mix of diarrhea, constipation, and foul-smelling gas.
Symptoms of SIBO
SIBO can present with a variety of symptoms, including:
Bloating and distension (worse after meals)
Excessive gas (belching or flatulence)
Abdominal pain or cramping
Diarrhea or constipation (or alternating between both)
Food intolerances (especially to fermentable carbohydrates)
Nutrient deficiencies (B12, iron, magnesium, fat-soluble vitamins)
Brain fog and fatigue
Unintentional weight loss or gain
Root Causes of SIBO
Functional medicine focuses on identifying and addressing the underlying causes of SIBO, including:
1. Impaired Gut Motility
The small intestine has a natural cleansing mechanism called the Migrating Motor Complex (MMC), which helps move bacteria out of the small intestine. If motility is impaired, bacteria can accumulate.
Common causes:
Chronic stress
Previous food poisoning (can damage the MMC)
Hypothyroidism (slows gut motility)
Chronic constipation
Functional Medicine Solution:
Support motility with prokinetics (ginger, 5-HTP, low-dose naltrexone)
Avoid snacking between meals to allow the MMC to function properly
Address underlying thyroid dysfunction
2. Low Stomach Acid (Hypochlorhydria)
Stomach acid helps kill bacteria before they reach the small intestine. Low stomach acid can allow bacterial overgrowth.
Common causes:
Proton Pump Inhibitor (PPI) use
Chronic stress
Aging
H. pylori infection
Functional Medicine Solution:
Support digestion with betaine HCl and digestive enzymes (if appropriate)
Reduce stress to improve stomach acid production
Test for and treat H. pylori if present
3. Gut Dysbiosis and Previous Infections
Disruptions in the balance of good and bad bacteria can contribute to SIBO.
Common causes:
Antibiotic overuse
Poor diet (high in sugar and processed foods)
Frequent infections (H. pylori, parasites, Candida)
Functional Medicine Solution:
Use herbal antimicrobials (berberine, oregano oil, allicin, neem) instead of broad-spectrum antibiotics when appropriate
Restore gut balance with probiotics and prebiotics
4. Structural Issues and Surgeries
Scarring from surgery or anatomical abnormalities can lead to bacterial stagnation in the small intestine.
Common causes:
Abdominal adhesions (from C-sections, endometriosis, or surgeries)
Diverticula (pockets in the small intestine where bacteria can grow)
Functional Medicine Solution:
Work with a practitioner to assess for anatomical issues
Consider visceral manipulation or physical therapy for abdominal adhesions
How is SIBO Diagnosed?
Functional medicine uses breath testing to measure gas levels produced by bacterial fermentation:
Lactulose Breath Test: Measures hydrogen and methane gas levels
Trio-Smart Test: Measures all three gases (hydrogen, methane, and hydrogen sulfide)
Functional Medicine Approach to SIBO Treatment
1. Starve the Overgrowth (Dietary Strategies)
Low-FODMAP Diet: Removes fermentable carbohydrates that feed SIBO bacteria.
Elemental Diet: A liquid-only diet that starves bacteria while providing essential nutrients.
Specific Carbohydrate Diet (SCD): Limits starches and complex carbs to reduce fermentation.
2. Kill the Overgrowth (Antimicrobials vs. Antibiotics)
Instead of conventional antibiotics (rifaximin), functional medicine may use:
Berberine (effective for hydrogen SIBO)
Oregano oil (broad-spectrum antimicrobial)
Allicin (garlic extract) (effective for methane SIBO)
Neem and Atrantil (for methane-producing bacteria)
3. Repair the Gut Lining
After bacterial overgrowth is treated, gut healing is crucial:
L-Glutamine to restore gut lining integrity
Bone broth and collagen for mucosal repair
Zinc carnosine to reduce inflammation
4. Support Gut Motility (Prevent Relapse)
Prokinetics (ginger, 5-HTP, Iberogast) to enhance the Migrating Motor Complex
Meal spacing (3–5 hours between meals) to allow proper gut cleansing
Stress management (meditation, breathwork) to prevent nervous system dysregulation
5. Reintroduce Foods and Long-Term Gut Maintenance
Slowly reintroduce high-FODMAP foods while monitoring symptoms
Maintain a diverse, fiber-rich diet to support a healthy microbiome
Continue gut-friendly habits like chewing food thoroughly and avoiding processed foods
Final Thoughts: A Holistic Approach to SIBO
SIBO is a complex condition that requires a personalized, multi-faceted approach to treatment. Functional medicine focuses on:
Identifying and addressing the root causes (gut motility, stomach acid, infections)
Using targeted antimicrobials and dietary strategies instead of long-term antibiotics
Supporting gut healing and long-term microbiome balance
If you suspect you have SIBO, working with a functional medicine practitioner can help you develop a personalized treatment plan to restore gut health naturally.
Looking for expert guidance on healing SIBO? Our functional medicine clinic offers comprehensive gut testing and customized treatment plans. Contact us today to start your journey to better digestive health!
