SIBO, or Small Intestinal Bacterial Overgrowth, involves an abnormal increase in bacteria in the small intestine. Under normal circumstances, bacterial levels are considerably lower in the small intestine than in the large intestine. The small intestine’s thinner mucus layer, large absorptive surface and close interaction with the immune system mean that bacterial overgrowth may affect both intestinal function and immune responses. Reduced stomach acid, impaired intestinal motility and altered function of the ileocecal sphincter are factors that may contribute to SIBO. Chronic stress may affect several of these mechanisms through the vagus nerve and intestinal motility. SIBO can cause symptoms such as bloating, gas, abdominal pain, diarrhoea, constipation and nausea. Other symptoms may also occur through interactions between the intestinal immune system, bacterial metabolites and the bloodstream. The gut-brain axis is an important area of ongoing research. Scientists are investigating how gut bacteria and their products may influence both the immune system and the nervous system. Supporting intestinal motility through strategies such as stress management, regular moderate physical activity and healthy lifestyle habits may help support a more balanced environment in the small intestine.
What is bacterial overgrowth in the small intestine?
SIBO, or Small Intestinal Bacterial Overgrowth, means that there are abnormally high levels of bacteria in the small intestine. Because the small intestine is primarily designed for nutrient absorption and has a much thinner mucus layer than the large intestine, bacterial overgrowth can affect both intestinal function and the immune system.
In this article, we explain what SIBO is, why bacteria can move into the small intestine, which symptoms may occur, and how stress, intestinal motility and the gut’s natural protective mechanisms are connected.
What is SIBO?
SIBO stands for Small Intestinal Bacterial Overgrowth and refers to an abnormal overgrowth of bacteria in the small intestine.
Bacteria normally play an important role in the body. In the large intestine, for example, bacteria break down dietary fibres that our own cells cannot use and convert them into substances such as certain B vitamins and vitamin K.
The problem can arise when bacteria that normally belong in the large intestine are present in excessive amounts in the small intestine.
The small intestine does not have the same thick protective mucus layer as the large intestine. With bacterial overgrowth, bacteria can therefore come closer to the intestinal wall, and their products may affect both the intestine and the immune system.
Why should bacteria mainly be found in the large intestine?
The large intestine has two strong mucus layers that help keep bacteria in place and protect the intestinal wall.
This is important because bacterial surface structures contain substances such as lipopolysaccharides (LPS) and lipoteichoic acid (LTA). These can act as powerful inflammatory substances.
The mucus layers of the large intestine allow water and salts to pass into the bloodstream while helping keep bacteria and their products separated from the immune system and circulation.
The small intestine functions differently.
Why is the small intestine more sensitive?
The small intestine is designed to absorb nutrients such as amino acids, fatty acids, carbohydrates, vitamins and minerals into the bloodstream.
It therefore has only a relatively thin and loose mucus layer, which primarily helps food contents move through the digestive tract towards the large intestine.
The total absorptive surface of the gastrointestinal tract is estimated at around 40 square metres — roughly half the size of a badminton court — with the vast majority belonging to the small intestine.
By comparison, the surface area of the large intestine is approximately 2 square metres, while the mouth, oesophagus and stomach together account for less than 1 square metre.
With SIBO, bacteria themselves may consume amino acids, vitamins, minerals and other nutrients from food that would otherwise be available to the body.
SIBO can therefore be compared to a cuckoo chick taking resources at the expense of others.
How is the small intestine protected from too many bacteria?
Three important mechanisms normally help keep bacterial levels in the small intestine under control:
Protective mechanism | How it helps |
Stomach acid | Hydrochloric acid in the stomach helps eliminate bacteria that enter with food. |
Intestinal peristalsis | Wave-like intestinal movements help prevent food residue from remaining in the small intestine for too long. |
Ileocecal sphincter | The valve between the small and large intestine helps prevent bacteria from moving back into the small intestine. |
When one or more of these protective mechanisms are impaired, the risk of bacterial overgrowth may increase.
How can SIBO affect the immune system?
The small intestine contains a large number of immune cells. It has been estimated that up to 70% of the body’s immune cells are located along the intestinal wall.
An important part of this immune system is found in structures called Peyer’s patches. These small lymphoid structures help the body tolerate substances from food while also identifying and responding to potentially harmful microorganisms.
With SIBO, immune cells may be exposed to bacterial products such as LPS and LTA over an extended period. This may lead to continued immune activation and contribute to chronic inflammation.
Can stress contribute to SIBO?
Yes. Chronic stress is an important factor that has been associated with SIBO.
The ileocecal sphincter functions somewhat like a swinging door between the small and large intestine. It normally helps prevent bacteria from the large intestine from moving back into the small intestine.
The vagus nerve plays an important role in regulating gastrointestinal function. When the body is in a relaxed state, vagal activity supports normal digestive function.
Stress, on the other hand, can reduce vagal activity and affect intestinal motility and the function of the gastrointestinal tract.
What can cause SIBO?
Several factors may contribute to the development of SIBO.
Reduced stomach acid
Reduced stomach acid, including in association with long-term use of acid-suppressing medication, may make it easier for bacteria from food to survive and reach the small intestine.
Short-acting antacids, such as Samarin, and treatments such as Gaviscon for heartburn do not affect long-term stomach acid production to the same extent.
Impaired intestinal motility
Normal intestinal motility involves wave-like movements that regularly move digestive contents through the gastrointestinal tract.
Chronic stress can also affect intestinal motility. When normal peristaltic movements are impaired, food residue and bacteria may remain in the small intestine for longer, potentially creating conditions that favour bacterial overgrowth.
Food poisoning
Food poisoning caused by bacteria such as Campylobacter, Salmonella and Shigella has also been associated with the development of SIBO.
Research has also found an association between moderate alcohol consumption and SIBO.
How common is SIBO?
The prevalence of SIBO varies depending on the population studied and the diagnostic criteria used.
Scientific studies referenced in this article have reported that up to 40% of healthy individuals tested positive for SIBO. However, it remains unclear whether healthy individuals with a positive SIBO test subsequently develop chronic health problems.
In studies referenced here, up to 85% of people with IBS had SIBO. A higher prevalence of SIBO has also been observed among people using acid-suppressing medication.
What are the common symptoms of SIBO?
Symptoms can vary from person to person and may resemble those of other gastrointestinal conditions.
Common digestive symptoms
- Abdominal pain or cramps
- Bloating or a swollen abdomen
- Gas and belching
- Diarrhoea
- Constipation
- Nausea
- Heartburn or acid reflux
- Increased sensitivity to foods that were previously tolerated, such as cow’s milk, eggs or grains
Because these symptoms can have many different causes, it is important to consider and rule out other underlying conditions.
Other symptoms
SIBO may also be associated with low-grade systemic inflammation. Symptoms described in the article include:
- Fatigue
- Joint pain
- Muscle pain
- Food intolerance, including sensitivity to gluten
- Skin inflammation such as rosacea
- Depression or low mood
Can SIBO affect the brain?
The small intestine and brain communicate through what is known as the gut-brain axis.
Communication takes place through, among other pathways, nerve fibres connected to the vagus nerve and through the bloodstream.
This has led to growing scientific interest in how gut bacteria and their products may influence the nervous system.
Is there a connection between gut bacteria and Parkinson’s disease?
Research has shown that the protein α-synuclein, which is associated with Parkinson’s disease, can be found along the small intestine in people with the disease.
Finnish researchers have identified the bacterium Desulfovibrio, which produces substances including hydrogen sulfide, LPS and magnetite. Research has linked this bacterium to unfavourable aggregation of α-synuclein in close proximity to the small intestine.
One possible mechanism being investigated is that α-synuclein may travel from the gut to the brain through the nerve pathways connecting the intestine and brain.
Is there a connection between gut bacteria and Alzheimer’s disease?
Amyloid is a protein that can accumulate in the brain in Alzheimer’s disease.
Research referenced in this article has investigated how the bacterial toxin LPS from Bacteroides fragilis may contribute to amyloid deposition and aggregation in the brain. Bacterial components from Bacteroides fragilis have been observed in the plaques found in the brains of people with Alzheimer’s disease.
This is another area in which researchers are investigating how gut bacteria and their products may communicate with or influence the brain.
What can you do if you have SIBO?
The article highlights several approaches that may support intestinal function and reduce factors that can contribute to bacterial overgrowth.
1. Support intestinal motility
The migrating motor complex (MMC) is part of the intestine’s natural movement pattern and helps move contents through the small intestine.
Coffee after a meal, ginger and bitter herbs such as dandelion, gentian root and wormwood are mentioned as possible ways to stimulate intestinal motility.
Moderate physical activity may activate the vagus nerve and thereby support intestinal motility and normal function of the ileocecal sphincter.
2. Reduce stress
Mindfulness, yoga, meditation and deep breathing can help activate the vagus nerve.
Regular recovery and relaxation may therefore be an important part of supporting intestinal motility and function.
3. Exercise regularly
Regular, moderate physical activity, such as walking, can support normal intestinal function.
4. Pay attention to fibre intake
The article recommends avoiding excessive intake of dietary fibre when dealing with SIBO.
5. Intermittent fasting
Intermittent fasting, with approximately 16 hours between main meals, is mentioned as a method that may support intestinal motility.
Longer fasting programmes also exist.
It may also be beneficial to avoid frequent snacking between meals so that the small intestine has time to clear its contents.
6. Botanical supplements
Botanical supplements with antibacterial properties mentioned in the article include:
- Oregano oil
- Magnolia bark
- Garlic
- Jatoba bark
- Ginger
- Wormwood
GutClear® is a 100% botanical supplement developed with a focus on the small intestine.
Berberine, oregano oil and allicin are also mentioned as possible complementary options.
Scientific references
Up to 40% of the population may have SIBO — often without knowing it
Rezaie et al. (2017). Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. American Journal of Gastroenterology, 112(5):775–784.
Increased intestinal permeability may play a key role in autoimmune diseases such as Hashimoto’s, coeliac disease, MS and RA
Fasano, A. (2011). Zonulin and its regulation of intestinal barrier function: The biological door to inflammation, autoimmunity, and cancer. Physiological Reviews, 91(1):151–175.
Increased intestinal permeability has been associated with neurodegenerative diseases such as Alzheimer’s, Parkinson’s disease and ALS
Kowalski & Mulak (2019). Brain–Gut–Microbiota Axis in Alzheimer’s Disease. Nutrients, 11(12):2825.
Sampson et al. (2016). Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease. Cell, 167(6):1469–1480.e12.
Blacher, E., Bashiardes, S., Shapiro, H. et al. Potential roles of gut microbiome and metabolites in modulating ALS in mice. Nature 572, 474–480 (2019).
Wu, S., Yi, J., Zhang, Y. G., Zhou, J., & Sun, J. (2015). Leaky intestine and impaired microbiome in an amyotrophic lateral sclerosis mouse model. Physiological Reports, 3(4), e12356.
Increased intestinal permeability and the release of bacterial toxins have been associated with metabolic conditions such as type 2 diabetes and obesity
Cani et al. (2007). Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes, 56(7):1761–1772.
TMAO and inflammation
Leng X et al. Impacts of intestinal microbiota metabolite trimethylamine N-oxide on inflammation and endothelial dysfunction. Frontiers in Microbiology. 2025.
TMAO and cognitive impairment
Long C et al. Association of trimethylamine oxide and its precursors with cognitive impairment: a systematic review and meta-analysis. Frontiers in Aging Neuroscience. 2024.
TMAO, cognition and dementia
Yaqub A et al. Plasma trimethylamine N-oxide (TMAO): associations with cognition, neuroimaging, and dementia. Alzheimer’s Research & Therapy. 2024.
TMAO and neuroinflammation
Yang J et al. The Gut Microbiota Modulates Neuroinflammation in Alzheimer’s Disease: Elucidating Crucial Factors and Mechanistic Underpinnings. CNS Neuroscience & Therapeutics. 2024.
TMAO and multiple sclerosis
Cen Q et al. Unraveling multiple sclerosis: a hidden interaction between gut microbiota and their metabolites. Gut Microbes. 2025.
TMAO and cardiovascular risk
Tang, W. H. W., Wang, Z., Levison, B. S., Koeth, R. A., Britt, E. B., Fu, X., … Hazen, S. L. (2013). Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. The New England Journal of Medicine, 368(17), 1575–1584.
TMAO, red meat and atherosclerosis
Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., … Hazen, S. L. (2013). Intestinal microbial metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature Medicine.
TMAO and cardiovascular events after stroke
Haghikia, A., Li, X. S., Liman, T. G., Bledau, N., Schmidt, D., Zimmermann, F., … & Widera, C. (2018). Gut microbiota-dependent trimethylamine N-oxide predicts risk of cardiovascular events in patients with stroke. Arteriosclerosis, Thrombosis, and Vascular Biology, 38, 2225–2235.
TMAO and atherosclerosis
Zhu, Y., & Zuo, R. (2020). Gut microbiota in atherosclerosis: focus on trimethylamine N-oxide. Atherosclerosis.
TMAO and human health
Gatarek, P., Bryk, D., et al. (2021). Trimethylamine N-oxide (TMAO) in human health. Journal of Clinical Medicine.
TMAO and chronic inflammatory and degenerative diseases
Constantino-Jonapa, L. A., Espinoza-Palacios, Y., Escalona-Montaño, A. R., Hernández-Ruiz, P., Amezcua-Guerra, L. M., Amedei, A., & Aguirre-García, M. M. (2023). Contribution of Trimethylamine N-Oxide (TMAO) to chronic inflammatory and degenerative diseases. Biomedicines, 11(2), 431.
