Why SIBO is a secondary condition
Key Takeaways
SIBO usually develops because another condition or medication interferes with the systems that keep bacterial numbers low in the small intestine.
Several systems help prevent SIBO, including normal gut movement, stomach acid, digestive secretions, and the structure of the digestive tract.
Impaired intestinal motility is one of the most important drivers of SIBO.
A SIBO diagnosis explains what is happening, but does not necessarily tell you why SIBO developed.
Identifying and treating an underlying cause, when possible, is an important part of preventing SIBO recurrence.
When someone is diagnosed with small intestinal bacterial overgrowth (SIBO), treating the bacterial overgrowth is only part of the picture. Another important question on the road to remission is: Why did the overgrowth develop in the first place?
SIBO is almost always a secondary condition, meaning another problem has disrupted the systems that normally keep bacteria in the small intestine in balance. Understanding and addressing that underlying problem, when possible, may be important for both reaching and maintaining remission.
What Does “Secondary Condition” Mean?
A primary condition is generally the disease or disruption that begins a chain of events. A secondary condition develops as a consequence of those changes.
With SIBO, the bacterial overgrowth itself can cause significant symptoms and health consequences. However, something has usually changed the environment of the small intestine in a way that allows bacteria to accumulate.
The body has several natural systems that work together to prevent bacterial overgrowth in the small intestine. Together, these systems:
Clear food and bacteria from the small intestine
Control bacteria through stomach acid and digestive secretions
Help prevent bacteria in the large intestine from moving backward into the small intestine
Protect the intestinal lining and help regulate microbes through the immune system
SIBO becomes more likely when one or more of these protective systems no longer works as intended. Importantly, the underlying factor is not always obvious. Sometimes it can be identified and treated. In other cases, it may be permanent, difficult to modify, or never fully determined.
Although many different conditions can increase the risk of SIBO, they often do so by disrupting one or more of the gut’s natural protective systems. While the underlying diseases may differ, the pathways that lead to SIBO are surprisingly similar.
The Most Common Ways Primary Conditions Lead to SIBO
Problems with Gut Motility
IOne of the most important protections against SIBO is movement. Between meals, the small intestine produces a repeating pattern of contractions called the migrating motor complex (MMC).
The MMC is sometimes described as the small intestine’s “housekeeping” system. During fasting periods, these waves of contractions help sweep leftover food particles, secretions, and bacteria toward the colon.
If this movement becomes impaired, intestinal contents remain in the small intestine longer, giving bacteria more time and opportunity to multiply.
A wide range of conditions can interfere with intestinal motility, including:
Gastroparesis and other motility disorders
Diabetes, particularly when nerves controlling the digestive tract are affected
Systemic sclerosis (scleroderma) and other conditions affecting intestinal muscles or nerves
Parkinson’s disease and other neurological conditions
Post-infectious IBS, in which food poisoning may lead to changes in the nerves controlling intestinal motility
Medications that slow intestinal movement, including opioids and some anticholinergic medications
The relationship does not mean that everyone with one of these conditions will develop SIBO. Rather, impaired movement can remove one of the small intestine’s most important protections against bacterial accumulation.
Changes in Intestinal Anatomy
Sometimes the problem is not how the intestine moves but how it is structured.
Certain changes to the structure of the digestive tract can create places where food and bacteria collect instead of moving forward normally. Some changes can also make it easier for microbes from the colon to move backward into the small intestine.
Examples include:
Intestinal surgery, such as gastric bypass or procedures that create blind loops
Narrowing or blockage of the intestine, such as from scar tissue or inflammation
Damage to or removal of the ileocecal valve, the body’s barrier between the small and large intestines
These structural changes can slow the normal movement of intestinal contents or weaken the natural barriers that help keep bacteria in the right part of the digestive tract, increasing the risk of SIBO.
Conditions such as Crohn’s disease can also increase the risk of SIBO when inflammation, scarring, surgery, or altered motility change the normal structure or function of the intestine.
Changes in the Gut’s Chemical Defenses
The digestive system also uses chemistry to help control microbial growth.
Stomach acid is one of the first defenses. Its highly acidic environment kills or suppresses many microorganisms entering through the mouth.
Bile and pancreatic secretions also contribute to digestion and help limit microbial growth as food passes through the small intestine.
Conditions that substantially alter these defenses may therefore increase susceptibility to SIBO. Examples can include:
Atrophic gastritis and other causes of low stomach acid
Pancreatic insufficiency
Certain stomach or intestinal surgeries
Some medications that alter the gastrointestinal environment
The relationship between proton pump inhibitors (PPIs) and SIBO has been debated, with studies producing differing results. More recent meta-analytic evidence suggests an association, particularly with longer exposure, but PPIs should not be assumed to be the cause of SIBO in every person taking them.
Diseases Outside the Digestive Tract
One reason SIBO can be difficult to understand is that the underlying problem does not necessarily originate in the intestine. Conditions affecting the nervous system, muscles, metabolism, immune system, or connective tissue can indirectly change how the digestive tract functions.
SIBO has been reported at increased rates in people with conditions including diabetes, systemic sclerosis, Parkinson’s disease, chronic pancreatitis, cirrhosis, celiac disease, and others.
However, having one of these conditions does not mean you are guaranteed to develop SIBO.
For some diseases, there is a plausible and well-described pathway to SIBO. For others, researchers know that SIBO occurs more frequently but are still investigating why and whether SIBO is a cause, consequence, or simply a common coexisting condition.
Why Does Identifying the Underlying Problem Matter?
Treating the bacterial overgrowth and treating the condition that allowed it to develop are two different goals.
Antibiotics or an elemental diet may reduce bacterial overgrowth and help induce remission. But if the intestinal environment that allowed SIBO to develop remains unchanged, bacteria may eventually accumulate again.
Recurrence of SIBO is common. One contemporary review reports recurrence in up to 44% of patients within nine months after remission.
This does not mean recurrent SIBO is necessarily the result of inadequate treatment. Sometimes the underlying risk factor simply cannot be eliminated. A person with a permanent change to their digestive tract after surgery, for example, may continue to have an increased susceptibility to bacterial overgrowth.
That is why modern approaches to SIBO management generally consider three separate goals:
Identify and address an underlying or predisposing factor when possible.
Reduce existing bacterial overgrowth and associated symptoms.
Develop a strategy to maintain remission and manage recurrence.
The Takeaway
A diagnosis of SIBO can tell you if there is evidence of abnormal bacterial overgrowth in the small intestine. But it does not necessarily answer the question as to why the overgrowth developed in the first place.
For many patients, understanding SIBO means looking beyond the bacteria themselves and considering the systems that normally keep the small intestine in balance. Sometimes that search identifies a treatable problem. Sometimes the underlying condition can be managed but not eliminated. And sometimes no single cause is ever found.
Understanding SIBO as a condition that often develops downstream from another disruption helps explain why treatment may need to involve more than simply reducing bacteria and why recurrent SIBO does not always mean that the original treatment failed.
Key References
Barlow, G. M., & Pimentel, M. (2025). Modern concepts of small intestinal bacterial overgrowth. Current Opinion in Gastroenterology, 41(6), 399–408. https://doi.org/10.1097/MOG.0000000000001135
Pimentel, M., Saad, R. J., Long, M. D., & Rao, S. S. C. (2020). ACG clinical guideline: Small intestinal bacterial overgrowth. The American Journal of Gastroenterology, 115(2), 165–178. https://doi.org/10.14309/ajg.0000000000000501
Li, X., Feng, X., Jiang, Z., & Jiang, Z. (2021). Association of small intestinal bacterial overgrowth with Parkinson’s disease: A systematic review and meta-analysis. Gut Pathogens, 13(25). https://doi.org/10.1186/s13099-021-00420-w
Losurdo, G., et al. (2020). The influence of small intestinal bacterial overgrowth in digestive and extra-intestinal disorders. International Journal of Molecular Sciences, 21, 3531. https://doi.org/10.3390/ijms21103531
Quigley, E. M. M., Murray, J. A., & Pimentel, M. (2020). AGA clinical practice update on small intestinal bacterial overgrowth: Expert review. Gastroenterology, 159(4), 1526–1532. https://doi.org/10.1053/j.gastro.2020.06.090
Rezaie, A., Pimentel, M., & Rao, S. S. C. (2016). How to test and treat small intestinal bacterial overgrowth: An evidence-based approach. Current Gastroenterology Reports, 18(2), 8. https://doi.org/10.1007/s11894-015-0482-9
Roszkowska, P., et al. (2024). Small intestinal bacterial overgrowth (SIBO) and twelve groups of related diseases—Current state of knowledge. Biomedicines, 12, 1030. https://doi.org/10.3390/biomedicines12051030
Sharabi, E., & Rezaie, A. (2024). Small intestinal bacterial overgrowth. Current Infectious Disease Reports, 26, 227–233. https://doi.org/10.1007/s11908-024-00847-7
Sroka, N., et al. (2023). Show me what you have inside—The complex interplay between SIBO and multiple medical conditions—A systematic review. Nutrients, 15, 90. https://doi.org/10.3390/nu15010090
Takakura, W., & Pimentel, M. (2020). Small intestinal bacterial overgrowth and irritable bowel syndrome – An update. Frontiers in Psychiatry, 11, 664. https://doi.org/10.3389/fpsyt.2020.00664