DR. THOMAS BACHARACH

Specialist in General Medicine

🕑 Reading time: 3–5 minutes

👆 Key takeaways

• SIBO (small intestinal bacterial overgrowth) can affect more than just the gut—it may impact the entire body, including energy levels, mood, and performance.
• SIBO stands for “Small Intestinal Bacterial Overgrowth” and describes an overgrowth/misplacement of bacteria in the small intestine: too many (or unfavorable) bacteria are present where bacterial levels should normally be low.
• Fatigue in SIBO may be explained by nutrient deficiencies, gases & metabolic byproducts (hydrogen/methane), as well as irritation of the intestinal lining and a compromised gut barrier.

SIBO and Fatigue: Why Small Intestinal Bacterial Overgrowth Can Leave You Exhausted

1. What is SIBO?
2. IBS or SIBO?
3. Why SIBO causes fatigue: nutrient deficiencies, gases, and inflammation
4. Causes: How does SIBO develop?
5. Treatment: antibiotics, nutrition, and holistic approaches
6. 5 steps to reduce fatigue in SIBO
7. Summary
8. FAQs

1. What is SIBO?

Bloating, gas, abdominal pain and digestive issues such as diarrhea or constipation are part of daily life for many people—often accompanied by unexplained fatigue and exhaustion. In many cases, these symptoms are caused by small intestinal bacterial overgrowth, internationally known as SIBO (Small Intestinal Bacterial Overgrowth).

While the large intestine is naturally densely colonized by bacteria, the small intestine should contain comparatively few bacteria. With bacterial overgrowth, this balance is disrupted: bacteria that typically belong in the large intestine migrate into the small intestine, settle there, and interfere with digestion, nutrient absorption, and the gut barrier. The result is typical symptoms such as bloating, abdominal pain, and changes in bowel habits.

Exhausted, tired, “brain fog”—and your gut is acting up?

For many people, bloating, abdominal pain, and bowel issues are caused by small intestinal bacterial overgrowth (SIBO).

Dr. Thomas Bacharach shares his expertise to explain how SIBO can affect the entire body—and what next steps may be helpful.

Learn more here

2. IBS or SIBO?

SIBO is often mistaken for irritable bowel syndrome (IBS) because many symptoms overlap. Typical symptoms include:

• Gas, sometimes severe, often shortly after eating.
• Visible bloating (abdominal distension) that tends to worsen throughout the day.
• Abdominal pain or diffuse cramping, often in the mid or lower abdomen.
• Diarrhea, recurrent diarrhea, or alternating diarrhea and constipation.
• Constipation, especially with methane-producing microbes.
• Belching, a feeling of fullness, nausea, and a sensitive gut in daily life.

Many people also report fatigue, exhaustion, brain fog (lightheadedness, difficulty concentrating), and mood swings, even though symptoms are centered in the abdominal area. This symptom complex is what makes the condition so burdensome: not only the gut, but everyday life as a whole can suffer from the bacterial overgrowth.

3. Why SIBO causes fatigue: nutrient deficiencies, gases, and inflammation

Pronounced fatigue in SIBO can have several possible causes that may reinforce one another:

Cause: Nutrient deficiency:

• Mechanism: Bacteria metabolize food components before they can be absorbed or interfere with absorption.
• Effect: Deficiency of vitamins (B12, fat-soluble vitamins) and minerals; promotes fatigue and exhaustion. Reduces stress resilience.

Cause: Gases (methane/H₂):

• Mechanism: Bacteria ferment dietary carbohydrates into hydrogen and methane.
• Effect: Gases affect the nervous system; cause “brain fog” and lightheadedness.

Cause: Immune activation:

• Mechanism: Irritation of the intestinal mucosa (leaky-gut phenomenon), increase in inflammatory markers.
• Effect: Systemic exhaustion (fatigue) due to a persistently active immune response.

4. Causes: How does SIBO develop?

SIBO usually doesn’t have just “one cause”—it’s often the result of several factors that disrupt natural bacterial control in the small intestine. Commonly discussed causes and risk factors include:

• Reduced intestinal motility (peristalsis): Slower movement allows bacteria to migrate from the large intestine into the small intestine and remain there.
• Reduced stomach acid production: Stomach acid normally helps protect against excessive bacterial growth; if acid is reduced (e.g., by medication), risk increases.
• Prior surgeries / anatomical changes / fistulas in the gastrointestinal tract.
• Chronic diseases (e.g., diabetes) that can affect motility or neural regulation.
• Repeated or long-term antibiotic use, which may shift the microbiome.
• Stress, an unbalanced diet, and highly processed foods as amplifying factors (motility & gut environment).

5. Treatment: antibiotics, nutrition, and holistic approaches

Treating SIBO typically requires several building blocks. These may include:

• Medication-based therapies (e.g., antibiotics, depending on findings and medical assessment).
• Dietary adjustments or a time-limited, symptom-oriented diet (often Low-FODMAP-inspired) to reduce symptoms.
• Support for digestion and motility (e.g., enzyme supplements, prokinetics—depending on the individual situation). Meal-Spacing to support the work of the MMC (Migrating Motor Complex).
• Holistic factors: stress management, sleep hygiene, and physical activity to support motility and recovery.

6. 5 steps to reduce fatigue in SIBO

Checklist: What can you do about fatigue in SIBO?

1. Do a breath test (H2/methane) to clarify the cause. Is SIBO present?
2. Check nutrient status (vitamin B12, fat-soluble vitamins, minerals).
3. Focus on easily digestible foods; consider a Low-FODMAP approach if needed.
4. Improve sleep hygiene to reduce strain on the nervous system.
5. Regular movement and active stress management to support gut function and sleep.

7. Summary

Small intestinal bacterial overgrowth is more than “just” bloating and abdominal pain: it can affect digestion, nutrient absorption, and therefore the entire body—including energy levels. Anyone experiencing persistent symptoms such as bloating, diarrhea, constipation, IBS-like symptoms, and unexplained fatigue should consider SIBO as a possible underlying cause and pursue a well-founded diagnosis (e.g., breath testing and additional assessments).

8. FAQs

Sources:

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8. Zollikofer CL, et al. SIBO: “small intestinal bacterial overgrowth”. Zürich: Center for Gastroenterology; approx. 2019. (Review with information on pathophysiology, diagnostics, therapy).
9. MSD Manuals, Professional Version. Small Intestinal Bacterial Overgrowth (SIBO) – etiology, pathophysiology, symptoms, diagnosis, and prognosis. 2025. Available at: https://www.msdmanuals.com/de/profi/ [Accessed: 12 Jan 2026].