Why SIBO Develops: Root Causes and Contributing Factors for Bacterial Overgrowth

Small Intestinal Bacterial Overgrowth, or SIBO, does not happen for just one reason. It is not simply a bacterial infection that appears out of nowhere.

​SIBO develops when bacteria that normally belong in the large intestine begin to multiply excessively in the small intestine, where bacterial numbers are usually kept very low.

In a healthy digestive system, the small intestine contains relatively few bacteria, typically fewer than 1,000 organisms per millilitre. This allows food to be broken down and nutrients to be absorbed efficiently. When bacterial numbers increase beyond this level, those bacteria begin fermenting carbohydrates too early in the digestive process. This fermentation produces gases such as hydrogen and methane, which lead to many of the symptoms people associate with SIBO, including bloating, pain, altered bowel habits, and discomfort.

One of the most frustrating aspects of SIBO is how often it comes back. Research shows that around 45 percent of people experience a recurrence after completing antibiotic treatment. These relapse rates tell us something important. If treatment focuses only on reducing bacteria without addressing why the overgrowth happened in the first place, lasting improvement is unlikely.
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From a naturopathic perspective, SIBO is best understood as the result of underlying imbalances in digestive function. Certain conditions create an environment in the small intestine where bacteria are able to survive, multiply, and persist.

Impaired Gut Motility: The Central Driver of SIBO

Of all the contributing factors, impaired gut motility is one of the most important drivers of SIBO. The digestive tract is not a passive tube. It is a dynamic system of muscles and nerves that move food, bacteria, and waste forward in a coordinated way.

A key part of this process is the migrating motor complex, often referred to as the MMC. The MMC is a repeating pattern of contractions that occurs every 90 to 120 minutes during fasting, between meals. Its role is to sweep residual food particles and bacteria out of the stomach and small intestine and into the large intestine.
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When this process is disrupted, bacteria are more likely to remain in the small intestine and multiply over time.

Q. What is the main cause of SIBO?

A. The most important underlying cause of SIBO is impaired gut motility, particularly disruption of the migrating motor complex, which normally clears bacteria from the small intestine between meals.

Several factors can interfere with normal gut motility. Gastrointestinal infections are a common trigger. After food poisoning or gastroenteritis, some people develop long-term changes in gut movement. This is often referred to as post-infectious IBS and is strongly associated with SIBO.
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Medical conditions such as hypothyroidism, diabetes-related nerve damage, autoimmune connective tissue disorders, and chronic stress can also slow intestinal transit. When motility slows, food and bacteria spend more time in the small intestine, increasing fermentation and symptom severity.

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Low Stomach Acid and Digestive Secretions

Stomach acid, bile, and digestive enzymes all help regulate bacterial growth in the small intestine. When these secretions are reduced, bacteria are more likely to survive and multiply.
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Stomach acid acts as a protective barrier by killing bacteria that enter the digestive tract with food. When acid levels are low, more bacteria reach the small intestine intact.

Q. Can low stomach acid cause SIBO?

A. Yes. Low stomach acid allows more bacteria to survive passage through the stomach and reach the small intestine, increasing the risk of bacterial overgrowth and SIBO.

Low stomach acid may result from acid-suppressing medications, Helicobacter pylori infection, chronic stress, nutrient deficiencies, ageing, or structural changes following gastric surgery.
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Bile acids and digestive enzymes also play essential roles. Bile helps control bacterial populations, while enzymes reduce the amount of undigested food available for fermentation. When these systems are compromised, the small intestine becomes a more favourable environment for bacterial overgrowth.

Gut Infections and Food Poisoning as Triggers

For many people, SIBO begins after a single episode of food poisoning. Even when the acute infection resolves, long-term changes in gut function may persist.
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Certain foodborne bacteria can produce toxins that trigger an immune response. In some cases, the antibodies produced by the immune system mistakenly target proteins involved in gut movement. This immune response damages the gut’s pacemaker cells and disrupts normal cleansing waves.

​Symptoms often appear long after the initial illness, sometimes months or years later, which makes the connection difficult to recognise. This delayed onset is one reason SIBO is frequently mislabelled as a functional digestive disorder.

Q. Can food poisoning lead to SIBO?

A. SIBO can develop after food poisoning when immune-mediated nerve damage disrupts normal gut movement, allowing bacteria to accumulate in the small intestine over time.

Why SIBO Often Comes Back

One of the most common frustrations with SIBO is recurrence. Many people feel better during treatment, only for symptoms to return weeks or months later.

Q. Why does SIBO keep coming back?

A. SIBO often recurs because antibiotic treatment reduces bacteria temporarily but does not correct underlying problems such as poor gut motility, low digestive secretions, or ongoing medication use.

Antibiotics can reduce bacterial numbers, but they do not address the conditions that allowed bacteria to overgrow in the first place. If motility remains impaired or acid suppression continues, the small intestine remains vulnerable.
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From a naturopathic perspective, long-term improvement depends on restoring the digestive environment rather than repeatedly targeting bacteria alone.

Conclusion

SIBO develops due to identifiable disruptions in digestive function, not by chance. Impaired gut motility, low stomach acid, altered digestive secretions, prior infections, medications, stress, and chronic health conditions all contribute to bacterial overgrowth in the small intestine.
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Understanding these mechanisms helps explain why symptoms persist and why recurrence is common. Addressing the root causes creates the foundation for more stable digestive health and better long-term outcomes.

Related Articles:
1. What is SIBO
2. SIBO Symptoms

Contact Us

​​​​​​​Vanessa Winter
​Naturopath & Medical Herbalist
BHSc (Deans Award for Academic Excellence), BED, Adv.Dip.Nat., Adv.Dip.Herb.Med., NMHNZ
​Registered with Naturopaths and Medical Herbalists of NZ (NMHNZ)

References

1. https://www.ncbi.nlm.nih.gov/books/NBK546634/
2. https://www.msdmanuals.com/professional/gastrointestinal-disorders/malabsorption-syndromes/small-intestinal-bacterial-overgrowth-sibo
3. https://pmc.ncbi.nlm.nih.gov/articles/PMC3099351/
4. https://www.mdpi.com/2077-0383/14/13/4702
5. https://www.nature.com/articles/s41522-025-00848-x
6. https://e-acnm.org/journal/view.php?number=331
7. https://pmc.ncbi.nlm.nih.gov/articles/PMC10303511/