The Complete SIBO Healing Protocol

Small Intestinal Bacterial Overgrowth (SIBO) occurs when bacteria that normally live in the large intestine proliferate in the small intestine, causing gas, bloating, diarrhea, and malabsorption. This comprehensive protocol outlines the evidence-based approach to diagnosing and treating SIBO.

What is SIBO?

SIBO occurs when bacteria that normally live in the large intestine proliferate in the small intestine. The small intestine should have relatively few bacteria compared to the colon. When bacterial counts increase abnormally, they ferment carbohydrates, producing gas and other metabolites that cause symptoms.

Medical reference materials outline the diagnostic criteria and risk factors, while this clinical review discusses how conditions like motility disorders, structural problems, and medications (particularly proton pump inhibitors) increase SIBO risk.

Common Symptoms

• Chronic bloating (especially after meals)
• Gas and abdominal distension
• Diarrhea, constipation, or alternating
• Abdominal pain or cramping
• Malabsorption and nutrient deficiencies
• Food sensitivities (especially carbohydrates)
• Fatigue and brain fog
• Nausea
• Weight loss (in severe cases)

Step 1: Proper Testing

Accurate diagnosis is essential before starting treatment. The gold standard is the SIBO breath test, which measures hydrogen and methane gas produced by bacteria.

Types of SIBO

• Hydrogen-dominant SIBO: Causes diarrhea, rapid transit
• Methane-dominant SIBO (IMO): Causes constipation, slow transit (now called Intestinal Methanogen Overgrowth)
• Hydrogen sulfide SIBO: Causes diarrhea, sulfur burps (harder to test for)
• Mixed types: Combination of the above

Understanding which type you have is crucial because treatment protocols differ. Methane-dominant SIBO, for example, requires specific antimicrobials that target methane-producing archaea.

Step 2: Dietary Approach

Low FODMAP Diet (Temporary)

FODMAPs (Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols) are carbohydrates that bacteria ferment, producing gas and symptoms. A low FODMAP diet temporarily reduces bacterial fuel.

Low FODMAP foods:

• Proteins: Meat, fish, eggs, tofu
• Vegetables: Carrots, cucumbers, zucchini, bell peppers, tomatoes, lettuce, spinach, green beans
• Fruits: Bananas, blueberries, strawberries, oranges, grapes (small portions)
• Grains: Rice, quinoa, oats, gluten-free bread
• Fats: Olive oil, coconut oil, avocado oil, butter/ghee

High FODMAP foods to avoid temporarily:

• Garlic and onions
• Wheat, rye, barley
• Legumes and beans
• High-lactose dairy
• Apples, pears, watermelon, mangoes
• Cauliflower, mushrooms, asparagus
• Honey, agave, high fructose corn syrup

Additional Dietary Principles

• Adequate protein: 20-30g per meal for satiety and healing
• Healthy fats: Support nutrient absorption and reduce inflammation
• Cooked vegetables: Easier to digest than raw
• Smaller, frequent meals: Reduce digestive burden
• Avoid snacking: Allow MMC (migrating motor complex) to function

Step 3: Antimicrobial Protocol

Antimicrobials reduce bacterial overgrowth. Both prescription antibiotics and natural antimicrobials can be effective.

Prescription Options

• Rifaximin: Non-systemic antibiotic, targets hydrogen-producing bacteria
• Neomycin: Often combined with rifaximin for methane
• Metronidazole: For hydrogen sulfide SIBO

Natural Antimicrobials (Often as Effective)

For Hydrogen-dominant SIBO:

• Oregano oil: 150-300mg standardized extract (70-85% carvacrol)
• Berberine: 500mg, 2-3 times daily
• Neem: 500-1,000mg twice daily
• Allicin (garlic): 600-1,200mg daily

For Methane-dominant SIBO:

• Atrantil: Proprietary blend targeting methanogens
• Allicin + Oregano: Combination approach
• Berberine + Neem: Alternative combination

Protocol Duration: Typically 2-4 weeks. Rotate antimicrobials if doing multiple rounds.

Step 4: Prokinetic Support

Prokinetics are crucial for addressing the root cause of SIBO: impaired motility. The MMC (migrating motor complex) is the intestinal "cleansing wave" that sweeps bacteria from the small intestine to the colon. When MMC function is impaired, bacteria accumulate.

Natural Prokinetics

• Ginger: 250-500mg or fresh ginger tea
• 5-HTP: 50-100mg before bed (supports serotonin, which stimulates MMC)
• MotilPro: Supplement combining ginger, 5-HTP, and acetyl-L-carnitine
• Iberogast: Herbal blend supporting motility

Prescription Prokinetics

• Low-dose naltrexone (LDN): 1-4.5mg nightly
• Prucalopride: Serotonin agonist
• Low-dose erythromycin: 50mg at bedtime (antibiotic dose is 250-500mg)

Duration: Prokinetics should be continued for 3-6 months minimum, often longer-term.

Step 5: Digestive Support

Enzyme Support

• Comprehensive enzymes: Protease, lipase, amylase with each meal
• Betaine HCl + pepsin: If low stomach acid (test carefully)
• Bile support: Ox bile or TUDCA if needed for fat digestion

Why This Matters

Undigested food feeds bacteria. Proper digestion reduces bacterial substrate and symptoms.

Step 6: Gut Lining Repair

SIBO often causes intestinal permeability (leaky gut). Repair while treating the overgrowth:

• L-glutamine: 5-20g daily (divided doses)
• Zinc carnosine: 75-150mg daily
• Collagen/bone broth: 10-20g daily
• DGL (licorice root): 380-1,140mg before meals
• Aloe vera: 50-200mg inner leaf
• Slippery elm or marshmallow root: Soothing and protective

Step 7: Retest and Adjust

After completing the protocol (typically 6-12 weeks total), retest with SIBO breath test to confirm resolution. If still positive:

• Consider different antimicrobials
• Investigate underlying causes (structural issues, motility disorders)
• Address biofilms with specific enzymes
• Check for concurrent issues (Candida, parasites)

Underlying Causes to Address

SIBO recurrence is common (up to 50%) if underlying causes aren't addressed:

Common Root Causes

• Impaired MMC: Food poisoning, nerve damage, medications
• Low stomach acid: Chronic PPI use, aging, H. pylori
• Structural issues: Adhesions, diverticula, strictures
• Ileocecal valve dysfunction: Allows backflow from colon
• Chronic stress: Affects motility and digestion
• Thyroid dysfunction: Hypothyroidism slows motility
• Medications: PPIs, opioids, antibiotics

Lifestyle Factors

Eating Habits

• Chew thoroughly: Begin digestion in the mouth
• Eat in relaxed state: Activate parasympathetic nervous system
• Space meals 4-5 hours apart: Allow MMC to function
• Don't eat 3-4 hours before bed: Support overnight MMC
• Stay hydrated: Between meals, not with meals

Stress Management

• Vagus nerve exercises
• Deep breathing before meals
• Meditation or mindfulness
• Adequate sleep (7-9 hours)
• Gentle exercise (avoid overtraining)

What to Expect During Treatment

Die-Off Reactions (Herxheimer)

When bacteria die rapidly, they release toxins that can temporarily worsen symptoms:

• Increased bloating and gas
• Fatigue
• Headaches
• Brain fog
• Skin breakouts

Support detoxification:

• Increase water intake
• Support liver (milk thistle, NAC)
• Activated charcoal or bentonite clay (away from supplements)
• Epsom salt baths
• Start antimicrobials slowly

Post-Treatment Maintenance

After successful SIBO treatment:

1. Continue prokinetics: 3-6 months minimum
2. Gradually expand diet: Reintroduce FODMAPs slowly
3. Support microbiome diversity: Varied whole foods diet
4. Address underlying causes: Thyroid, stress, etc.
5. Monitor symptoms: Catch recurrence early
6. Probiotics (carefully): Some may worsen SIBO; choose wisely

Key Takeaways

• SIBO requires proper testing (breath test) before treatment
• Low FODMAP diet is temporary (4-8 weeks max)
• Antimicrobials (natural or prescription) reduce overgrowth
• Prokinetics are essential for addressing root cause and preventing recurrence
• Digestive support and gut lining repair are crucial
• Address underlying causes to prevent relapse
• Retest to confirm resolution
• Patience is key—healing takes time