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The Connection Between SIBO, Leaky Gut Syndrome, and Adverse Food Reactions

Updated: Apr 16

Digestive issues are becoming increasingly common, with many people struggling with bloating, discomfort, food reactions, and unexplained symptoms after eating. One of the most overlooked causes of these issues is Small Intestinal Bacterial Overgrowth (SIBO). While SIBO can lead to leaky gut syndrome and increase adverse food reactions, not all reactions are the same. Understanding the difference between bacterial fermentation reactions and immune system responses is key to identifying and treating the root cause of digestive distress.


SIBO and Its Impact on Digestion

SIBO occurs when an excessive amount of bacteria colonize the small intestine, an area that should normally have low bacterial levels. These bacteria ferment undigested food, producing excess gas (hydrogen, methane, or hydrogen sulfide) and metabolic byproducts that can damage the gut lining. The results:

  • Bloating, gas, and cramping due to fermentation.

  • Leaky gut syndrome, where the intestinal lining becomes permeable and allows toxins and food particles to enter the bloodstream.

  • Increased toxin loads (such as lipopolysaccharides (LPS), lactic acid, and ammonia), triggering inflammation and systemic symptoms.


SIBO can be diagnosed using a breath test, which measures the presence of hydrogen and methane gas produced by bacterial fermentation.


Leaky Gut Syndrome: The Missing Link

Leaky gut syndrome is not a disease itself but a condition where the tight junctions of the intestinal wall become compromised. This allows substances that should remain in the gut to leak into the bloodstream. This condition is often a consequence of chronic SIBO, gut infections, inflammation, or poor diet.


Once the gut barrier is weakened, the body is exposed to toxins, undigested food particles, and harmful bacteria. This exposure leads to immune system activation and increased food sensitivities.


Differentiating Food Reactions: Bacterial Fermentation (SIBO) vs. Immune System Responses (Allergy/ Sensitivity)

Not all food reactions are caused by allergies or sensitivities. Understanding the distinction between bacterial fermentation and immune-mediated food reactions helps guide proper testing and treatment.


Bacterial Fermentation Reactions (SIBO-Related Food Reactions)

  • Cause: Overgrown bacteria ferment carbohydrates and produce gas

  • Symptoms: Bloating, gas, cramping, diarrhea, or constipation

  • Onset: Within 30 minutes to a few hours after eating fermentable foods

  • Common Triggers: High-FODMAP foods such as onions, garlic, apples, wheat, dairy, and legumes

  • Diagnosis: SIBO breath test (lactulose or glucose breath test)


Immune System Reactions (Allergies & Sensitivities)

  • Cause: The immune system overreacts to select food proteins

  • Symptoms: Range from digestive issues (bloating, nausea, diarrhea) to systemic symptoms like fatigue, headaches, joint pain, and skin reactions

  • Onset: Can be immediate (IgE allergies) or delayed by hours or even days (IgG or IgG4 sensitivities)

  • Common Triggers: Dairy, gluten, eggs, soy, nuts, shellfish

  • Diagnosis: Food allergy/sensitivity blood test (testing IgE, IgG4, IgG, and CA3 levels to 88 foods)


Table contrasting symptoms of leaky gut caused by bacterial fermentation vs immune system reactions

Why Testing Matters

Because bacterial overgrowth and immune reactions can coexist, proper testing is crucial to distinguish between them and develop an effective treatment plan.


  • SIBO Breath Testing identifies bacterial fermentation issues.

  • Food Allergy/Sensitivity Blood Testing assesses immune-mediated food reactions.


Without testing, many people eliminate foods unnecessarily or treat the wrong cause of their symptoms, leading to frustration and ongoing digestive distress.


Treating SIBO, Leaky Gut, and Food Sensitivities

Treat the Root Cause: SIBO

  • Herbal antimicrobials or antibiotics (such as Rifaximin) can reduce bacterial overgrowth.

  • Following a low-FODMAP or SIBO-specific diet can temporarily ease symptoms while treating overgrowth.


Heal the Gut Barrier

  • L-glutamine, zinc, collagen, and probiotics support gut lining repair.

  • Addressing inflammation helps restore gut integrity.


Manage Food Sensitivities

  • Short-term elimination of problematic foods based on IgE, IgG, IgG4, and CA3 testing.

  • Gradual reintroduction after gut healing to determine tolerance.


Final Thoughts

SIBO, leaky gut syndrome, and adverse food reactions are deeply interconnected. Chronic bloating, gas, digestive issues, and systemic symptoms can stem from bacterial overgrowth, immune responses, or both. By using breath testing for SIBO and blood testing for food reactions, individuals can uncover the root cause of their symptoms and receive the most effective treatment.


If you're struggling with digestive issues and suspect SIBO or food sensitivities, consider getting tested to take the first step toward long-term gut health and symptom relief. Contact us to schedule an appointment.


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