When people are diagnosed with small intestinal bacterial overgrowth (SIBO), it’s natural to assume that SIBO itself is the main problem. However, SIBO is a secondary condition, meaning it develops because another disease or disruption has changed how the digestive system normally works. Understanding this distinction helps explain why SIBO often returns and why treatment sometimes needs to go beyond reducing bacteria alone.

What Does “Secondary Condition” Mean?

A primary disease is the main condition affecting the body. It is the starting point of a problem.

A secondary condition develops as a consequence of that primary disease. It reflects downstream effects rather than an independent cause.

SIBO is secondary because it arises when the gut’s natural defenses against bacterial overgrowth are compromised. These defenses include:

• Normal gut movement (motility)

• Stomach acid and digestive enzymes

• The immune system

• Physical barriers, such as the ileocecal valve

When one or more of these systems stops working properly, bacteria are more likely to accumulate in the small intestine.

The Most Common Ways Primary Conditions Lead to SIBO

Disrupted Gut Motility

Impaired gut movement is the most common driver of SIBO. When food and bacteria are not cleared efficiently, they linger and multiply.

Conditions that affect nerves, muscles, or coordination in the gut can slow motility, including autoimmune, neurological, metabolic, and hormonal disorders. In these cases, SIBO develops because the gut can no longer “self-clean” effectively.

Structural or Anatomical Changes

Physical changes to the digestive tract can also create areas where food and bacteria collect.

Examples include digestive surgeries that alter normal anatomy, loss of the ileocecal valve, or inflammatory bowel disease with strictures or scar tissue. These changes remove mechanical barriers that normally help keep bacteria in the right place and/or moving smoothly through the digestive system.

Weakened Chemical or Immune Defenses

The gut relies on chemical and immune defenses to control bacteria. SIBO risk increases when stomach acid is reduced, digestive juices or bile acids are impaired, or immune signaling in the gut is altered. When the gut environment changes, bacteria that would normally be controlled can survive and overgrow.

The Cycle of SIBO

Once SIBO develops as a secondary condition, it often worsens the underlying problem.

Bacterial overgrowth can interfere with nutrient absorption, increase inflammation, disrupt bile acids, and increase intestinal permeability. These effects can aggravate symptoms of the primary disease, creating a feedback loop where SIBO and the underlying condition reinforce each other.

This is one reason SIBO can be difficult to treat if the root cause is not also addressed.

The Takeaway

Understanding SIBO as a secondary condition is key to understanding why a SIBO diagnosis cannot identify the root cause of symptoms. For many people, symptoms may continue to occur until the primary condition is identified and addressed.