SIBO (Small Intestinal Bacterial Overgrowth): Symptoms, Causes & Evidence-Based Treatment Guide

SIBO occurs when excessive bacteria colonize the small intestine, disrupting digestion, nutrient absorption, and systemic health. Unlike the colon, which hosts trillions of microbes, the small intestine typically maintains a low bacterial count. Overgrowth here triggers a cascade of metabolic and immune dysfunction. Below, we dissect SIBO's mechanisms, risk factors, and clinical implications.

N.b. This article is intended as an international self-study guide. It does not replace or provide medical advice or treatment. Do not start any supplement or herb without first evaluating possible interactions with drugs. Always discuss the treatment of intestinal diseases with your doctor.

Introduction

Small intestinal bacterial growth (SIBO) means an excess of bacteria growing in the small intestine. Although many doctors do not yet recognize SIBO as a medical diagnosis, it has accumulated a significant quantity of medical research over the last 10 years, leading to increased knowledge of the existence of SIBO.(1) Normally, only small amounts of bacteria grow in the small intestine. Most bacteria live in the colon (large intestine). However, there are situations where the level of bacteria in the small intestine may increase to harmful levels and lead to many serious health problems.

What Is SIBO?

The small intestine's primary role is nutrient absorption. Bacterial overgrowth in the small intestines:

Ferments carbohydrates, producing hydrogen/methane gas.
Damages the gut lining, impairing nutrient uptake (e.g., iron, B12).
Triggers inflammation and exacerbates systemic issues like fatigue or joint pain.

The symptoms caused by SIBO are often similar to those caused by other causes of gut problems. Therefore, IBS and SIBO are often mixed. In fact, according to a scientific meta-analysis published in 2009, 54 % of IBS patients have SIBO.(2) According to a survey published in 2017, 4–78 % of IBS patients and 1–40 % of "healthy" controls suffer from SIBO.(3)

HEALTH FACTORS PREDISPOSING ONE TO SIBO:(4-5)

Reduced gastric acid production or hypochlorhydria, an acid-free stomach or achlorhydria, caused, for example, by continuous use of proton pump inhibitors (PPIs)
Small intestinal motility disorders
Disorders of pancreatic digestive enzyme production
Small intestinal diverticula
Systemic diseases (celiac disease, Crohn's disease, fatty liver)
Intestinal surgery
Intestinal blocks (strictures, tumors, ulcers)

Other factors associated with SIBO in IBS patients include aging and female gender and predominance of bloating, flatulence and diarrhea.(6)

Key Causes & Risk Factors of SIBO

Factor	Mechanism	Examples
Impaired Motility	Slowed intestinal movement allows bacterial stagnation	Diabetes, scleroderma, opioid use
Anatomical Abnormalities	Structural issues (e.g., strictures, surgeries) trap bacteria	Gastric bypass, Crohn’s disease
Low Stomach Acid	Reduced acid fails to sterilize the upper GI tract	Chronic PPI use, aging
Dysbiosis	Gut microbiome imbalance favors pathogens	High-sugar diets, antibiotic overuse
Chronic Stress	Alters gut-brain axis signaling and motility	Anxiety, prolonged cortisol spikes

Symptoms & Clinical Presentation

SIBO symptoms overlap with IBS and other GI disorders, making diagnosis challenging.

Diarrhea (hydrogen is dominant in gas formation)
Constipation (methane is dominant in gas formation)
Flatulence
Intestinal cramps and pains
Systemic general symptoms such as fatigue, joint pain, anxiety, and depression are often caused by the release of bacterial neurotoxins (mainly constipation-prone SIBO)

THE SIBO PATH: Bacterial overgrowth –> Hydrogen gas –> Arcanobacterial overgrowth –> Methane gas

When bacteria ferment fibers, they produce hydrogen gas. Similarly, so-called arcanobacteria live on hydrogen and produce methane gas. Methane is usually associated with constipation-prone bacterial overgrowth, while diarrhea-prone bacterial overgrowth is caused by hydrogen. Hydrogen-dominant SIBO is usually easier to treat than methane-dominant SIBO.

Diagnosis

Breath Testing:
- Measures hydrogen/methane after consuming lactulose or glucose.
- Limitation: False negatives occur if bacteria reside deep in the small intestine.
Clinical Correlation: Symptoms + risk factors (e.g., PPI use, prior abdominal surgery).

Image: An example report of SIBO breath test.

Treatment Protocols

Before jumping into the treatment protocol, it is recommended that a lab test be done to determine the possibility of SIBO (see above). Options are either 2-hour or 3-hour assessments. The 3-hour SIBO profile provides insight into gas levels over a longer time and is recommended for patients with slower gastrointestinal transit or constipation. Also, the gastric hydrochloric acid production (e.g., Gastropanel lab test and self-produced gastric hydrochloric acid test) should be evaluated.(7)

If there is a clear indication of SIBO in the test, the following protocol is science-based and effective.

1️⃣ Antibiotic Therapy (8)

Rifaximin: 550 mg 3x daily for 14 days (non-absorbed antibiotic with minimal side effects).
Combination Therapy: Rifaximin + neomycin for methane-dominant cases.
Pre-Treatment Strategy: Consume FODMAPs 1–2 weeks before antibiotics to activate bacterial targets.

N.b. Antibiotics require a medical doctor's prescription.

2️⃣ Herbal Protocols (9-11)

Herbal regimens show efficacy comparable to antibiotics:

Protocol	Dosage	Duration
FC Cidal + Dysbiocide	2 capsules, 2x daily	4 weeks
Candibactin-AR + Candibactin-BR	2 capsules, 2x daily	4 weeks
Atrantil	Follow label instructions	4–8 weeks

3️⃣ Dietary Interventions (12-13)

Low FODMAP Diet: Reduces fermentable carbs (e.g., onions, garlic, legumes, gluten grain) to starve bacteria. Implement in phases:
1. Elimination: 2–6 weeks.
2. Reintroduction: Identify trigger foods.
3. Personalization: Maintain long-term tolerance.
Ketogenic Diet: Limits carbs to <50 g/day, reducing bacterial fuel. Effective for diarrhea-predominant cases.

Too long or short meal spacing can exacerbate symptoms; the optimum would be 3–4 hours between meals (except nighttime). On the other hand, in some situations, fasting and intermittent fasting may also help. Limit caffeine intake (e.g. up to 1–2 cups of coffee daily).

4️⃣ Probiotics & Gut Support

Targeted Strains:
- Bifidobacterium infantis 35624: Reduces IBS symptoms.(14)
- Lactobacillus rhamnosus GG: Competes with pathogens.(15)
Prebiotics: Avoid during active SIBO; reintroduce post-treatment (e.g., PHGG, resistant starch).

N.B. Be careful with probiotics, especially if you have or have had SIBO and brain fog due to the condition. Particularly so-called D-lactic acid-producing probiotic strains (such as Lactobacilli) may be harmful,(16) since D-lactic acidosis is common in patients with brain fog.(17)

5️⃣ Adjunctive Therapies & Re-testing

Prokinetics: Prescribed to prevent recurrence (e.g., low-dose erythromycin).
Peppermint Oil: Reduces spasms and bloating (enteric-coated capsules, 0.2–0.4 mL 3x daily).

After 4 weeks, test your bacterial overgrowth with a new breath test; if the treatment is successful, you can gradually and incrementally restore fiber and FODMAP carbohydrates to your diet.

The small intestine should have very little bacteria growth and no yeast growth. Medical publications have also disclosed observations of the "small intestinal overgrowth of yeast" or SIFO (Small Intestinal Fungal Overgrowth). Many people with SIBO may also have SIFO, which means that there is too much yeast (usually Candida varieties) in the small intestine.(18)

Pathophysiology: How SIBO Harms Health

Nutrient Malabsorption :
- Bacteria consume B12, iron, and carbohydrates, leading to deficiencies.
- Damaged enterocytes reduce enzyme production (e.g., lactase).
Leaky Gut :
- Bacterial toxins (e.g., LPS) breach the intestinal barrier, triggering systemic inflammation.(19-20)
Neurotransmitter Disruption :
- Gut microbes influence serotonin and dopamine production, linking SIBO to anxiety/depression.(21-22)

The Gut-Brain Axis Connection

The vagus nerve and microbial metabolites (e.g., short-chain fatty acids) create a bidirectional communication loop:

Stress → SIBO: Chronic stress slows motility, fostering bacterial overgrowth.
SIBO → Mood Disorders: Bacterial LPS and inflammatory cytokines cross the blood-brain barrier, altering neurochemistry.(23-24)

Prevention & Long-Term Management

While treatment protocols exist, prevention focuses on the following main things:

Dietary Hygiene: Avoid excess sugar, refined carbs and processed fats.
Motility Support: Intermittent fasting, ginger/artichoke extracts.
Stress Resilience: Breathwork, vagus nerve stimulation.

SIBO exemplifies the gut's role as a metabolic, immune, and neurological health nexus. Addressing it requires a systems-level approach, blending microbial ecology with lifestyle optimization.

Conclusion

SIBO arises from bacterial overgrowth in the small intestine, disrupting digestion, nutrient absorption and systemic health. Symptoms like bloating, diarrhea/constipation, fatigue, and neurological issues (e.g., brain fog, anxiety) stem from bacterial fermentation, gut lining damage, and inflammatory toxin release. Diagnosis hinges on breath testing and clinical risk factors (e.g., PPI use and motility disorders).

Treatment prioritizes targeted antimicrobials (Rifaximin ± neomycin), dietary strategies (low-FODMAP/ketogenic protocols), and post-therapy microbiome support with strain-specific probiotics (e.g., Bifidobacterium infantis) to prevent relapse. Chronic stress exacerbates SIBO by impairing gut motility, while bacterial metabolites like LPS disrupt the gut-brain axis, linking SIBO to mood disorders. Long-term management requires dietary hygiene (avoiding refined carbs/sugars), motility enhancers (intermittent fasting, ginger), and vigilance for co-occurring fungal overgrowth (SIFO) or nutrient deficiencies.

Addressing SIBO demands a holistic approach—balancing microbial ecology, personalized nutrition and stress resilience—to restore gut integrity and systemic equilibrium.

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