SIBO: What Lies Behind the Condition Mistaken for a Disease, Part 2

Diet and Nutrition, General Health, Your Very Special Child
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The second part of the article focuses on the diagnosis of Small Intestinal Bacterial Overgrowth (SIBO), continuing the discussion of essential topics not covered in Part One. In that part, we reviewed the core symptoms and causes of SIBO. Now we focus on diagnostic tools that help identify this condition and guide optimal therapy. Distinguishing between the different types of SIBO — hydrogen, methane, and hydrogen sulfide — requires accurate diagnostic methods to select the correct treatment. Importantly, diagnosing SIBO not only confirms the condition but helps rule out other diseases with similar symptoms.

SIBO Diagnosis

Three Types of SIBO:

  • Hydrogen SIBO: This type is commonly associated with diarrhea. Bacteria in the small intestine ferment carbohydrates, producing hydrogen gas, which leads to poor digestion and faster bowel movements.
  • Methane SIBO: More often linked to constipation. It involves methane-producing bacteria that slow down intestinal motility, causing stool retention and constipation.
  • Hydrogen Sulfide SIBO: Often associated with diarrhea but may also cause constipation. Hydrogen sulfide is a gas produced by certain bacteria and can have toxic effects on the gut, triggering symptoms similar to other forms of SIBO.

Why Diagnosis Matters

Identifying the type of SIBO is essential for choosing the right treatment. Measuring the type and concentration of gas (hydrogen, methane, or hydrogen sulfide) allows physicians to understand the dominant microbial population and tailor the therapy accordingly.

SIBO is diagnosed using the lactulose breath test. The patient drinks a lactulose solution, which serves as a substrate for bacteria in the small intestine. If bacteria are present, they ferment this sugar, producing gas. The test measures the levels of hydrogen and methane in exhaled breath:

  • A hydrogen rise of more than 20 ppm within the first 2 hours confirms hydrogen-dominant SIBO.
  • Methane levels above 10 ppm at any point indicate methane-dominant SIBO.
  • A newer test is available to detect hydrogen sulfide specifically.

SIBO contributes to inflammation and leaky gut syndrome.

  • Leaky gut diagnostics: Elevated zonulin and secretory IgA in stool samples indicate inflammation and compromised gut barrier integrity.

SIBO Treatment

Importance of Treating the Root Cause

SIBO is often a secondary condition, linked to other diseases or disorders. For effective and long-lasting treatment, it’s essential to address the underlying root cause. Without doing so, therapy may fail and SIBO may recur.

Stress is a major contributor to SIBO because it disrupts the intestinal migrating motor complex (MMC) — the wave-like contractions that cleanse the small intestine between meals. When this function is weakened, bacteria can accumulate and proliferate.

Moreover, untreated SIBO can lead to other diseases. In fact, SIBO is the root cause in approximately 70% of IBS cases, and IBS affects about 25% of the global population.

The Three Stages of SIBO Treatment:

  • Starving the bacteria with a specialized diet:

    • A low-FODMAP, low-lectin diet restricts carbohydrates that bacteria can ferment, reducing bacterial load and easing symptoms. The diet usually lasts about 1 month, followed by gradual food reintroduction.
    • FODMAPs (Fermentable Oligo-, Di-, Mono-saccharides And Polyols) cause fermentation and gas production. High-FODMAP foods: beans, dairy, asparagus, artichokes, garlic, onions. You can use the SIBO Specific Diet: Food Guide.
    • Lectins are plant defense compounds found in legume skins, whole grains, and seeds. High-lectin foods: tomatoes, cucumbers, peppers, eggplants, beans, whole grains. Notably, gluten-containing grains (wheat, barley, rye) are rich in lectins. Exception: white basmati rice is lectin-free and easily digested.

  • Killing the bacteria using antimicrobials:

    • Antibiotics such as rifaximin or herbal antimicrobials (berberine, oregano, allicin) are used to reduce bacterial overgrowth. The choice depends on clinical preference.

  • Stimulating intestinal motility:

    • Maintain 4–5 hour intervals between meals to support the Migrating Motor Complex (MMC).
    • Intermittent fasting for 14–18 hours promotes MMC activity and allows deeper intestinal cleansing.
    • Use of prokinetics, such as magnesium citrate and vitamin C, may improve motility and prevent stagnation.
    • Daily bowel movements are essential for preventing bacterial buildup.
    • Frequent snacking disrupts MMC activation. Constant eating keeps the intestines in digestion mode and hinders the cleaning waves, allowing bacteria and residue to build up.

  • Restoring gut microbiota:

    • Use targeted prebiotics and probiotics (especially spore-based) to rebalance gut flora and enhance barrier function.
    • Healing leaky gut focuses on restoring mucosal integrity, reducing inflammation, and improving microbiome health.
    • Digestive enzymes help break down food more efficiently, depriving SIBO bacteria of nutrients.

  • Lifestyle Adjustments

    • Stress management is vital, as stress significantly affects gut motility and digestion. Developing effective stress-reduction strategies is essential.
    • Meal timing: Maintain regular meals to support digestive rhythm and prevent stagnation.

These stages provide a comprehensive approach to addressing SIBO and restoring normal intestinal function.

Not All Gut Issues Are SIBO

Everyone who made it this far and experiences symptoms similar to SIBO might think that this is exactly their issue. However, SIBO is just one possible cause — and one that many people haven’t heard of before. That’s why proper diagnosis is essential: to understand what’s really behind your symptoms. Below are several conditions that may mimic SIBO, but have different root causes and therefore require different diagnostic and treatment approaches.

SIFO (Small Intestinal Fungal Overgrowth)

SIFO often presents with symptoms that resemble those of SIBO — bloating, abdominal pain, irregular bowel movements, and gas.

  • Diagnosing SIFO is based on clinical signs and lab testing:

    • Stool testing can reveal fungal overgrowth (e.g., Candida), which may indicate microbial imbalance.
    • Breath tests are not effective for diagnosing SIFO because they are designed to detect bacterial overgrowth, not fungal.

  • Treating SIFO involves:

    • Diet: Eliminating foods that promote fungal growth (sugar, grains, dairy, alcohol, and high-glycemic fruits).
    • Antimicrobials and antifungals: Herbal agents and pharmaceutical antifungal medications are used to combat fungal overgrowth.
    • Probiotics and beneficial yeasts: Saccharomyces boulardii is effective in displacing Candida.

Other Conditions That May Mimic SIBO Symptoms

  • Irritable Bowel Syndrome (IBS): While often co-occurring with SIBO, IBS itself is not caused by bacterial overgrowth.
  • Gastroenteritis: Symptoms are due to infections by pathogens (bacteria, viruses, or parasites) but unrelated to bacterial overgrowth.
  • Lactose or fructose intolerance: Caused by enzyme deficiencies, leading to sugar fermentation, but not microbiota imbalance.
  • Celiac disease: Damages the villi of the small intestine, resulting in malabsorption, bloating, and diarrhea — but not due to bacterial overgrowth.
  • Parasitic infections: For example, Giardia lamblia may cause similar symptoms (diarrhea, bloating), but is caused by a parasite rather than bacterial overgrowth.

Each of these conditions requires a specific treatment strategy. Mistaking them for SIBO can result in ineffective therapy, which is why accurate diagnosis is critical for appropriate and successful treatment.

The breath test for diagnosing SIBO can be performed through SIBO Diagnostics

Conclusion

Accurate SIBO diagnosis is essential for choosing the right treatment, as different types require different therapeutic approaches. Breath testing helps identify the dominant gas — hydrogen, methane, or hydrogen sulfide — guiding therapy selection. Comprehensive treatment that includes diet, antimicrobials, and microbiota restoration is effective for reducing symptoms and preventing recurrence. Accurate diagnosis also helps rule out other conditions with similar symptoms, supporting a successful path to gut healing.