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Are Probiotics Effective in Managing Small Intestine Bacterial Overgrowth (SIBO)?

Updated: Jan 4

The small intestine contains different bacteria that help in the absorption and digestion of food which is considered a good bacterium. Whereas there are some conditions when instead of good bacteria, certain types of bad bacteria are grown inside the small intestine that restricts food digestion and absorption.

Small Intestine Bacterial Overgrowth (SIBO) refers to the imbalance in the bacterial content of the small intestine such that the good bacteria either don’t function properly or the growth of bad bacteria becomes more rapid than usual.

Probiotics are considered an effective approach to managing and treating Small Intestine Bacterial Overgrowth (SIBO), but certain factors need to be considered before administering or prescribing the probiotics [1].

Physiological overview of SIBO

To understand the relationship between probiotics and SIBO, it is important to discuss the physiology behind SIBO.

SIBO occurs when the bacterial population in the small intestine is abnormally increased such that the quantity of Escherichia coli, Klebsiella pneumonia, Enterococcus spp., and Proteus mirabilis bacteria is doubled. The overgrowth of these bacteria leads to the excessive fermentation of the carbohydrates, fibers, and starch content of the food due to which the by-product gases are formed resulting in damage to the intestinal walls making it difficult for the food to be digested or absorbed. The imbalanced increased growth of small intestine bacteria leads to medical symptoms such as bloating, diarrhea, constipation, or abdominal pain [2].

A recent study shows that SIBO is more likely to be diagnosed when a patient is reported with other gastrointestinal problems as SIBO is often associated with other medical conditions such as irritable bowel syndrome (IBS). Certain lab diagnosis is required to investigate the occurrence of SIBO which include lactulose or glucose breath test, small intestine aspirate, fluid culture test, stool test, and lactulose breath test. These lab testing help a physician to confirm the occurrence of SIBO [3]. However, some researchers suggest that more than one-third of IBS patients are diagnosed with SIBO, and most physicians prescribe SIBO antibiotics when treating IBS.

Depending on the type of bacterial overgrowth, SIBO is categorized based on different types of gases produced including methane-dominant SIBO, Hydrogen dominant SIBO, and Hydrogen Sulphide SIBO. It is also possible that multiple gases may be produced at a time i.e. methane and hydrogen, then the condition is called “mixed type SIBO”. Methane-dominant SIBO often causes severe constipation whereas hydrogen-dominant SIBO often causes diarrhea and hydrogen sulfide SIBO is linked with diarrhea and abdominal pain [1].

Treatment of SIBO with probiotics

A lot of research evidence claimed that probiotics are more effective than SIBO antibiotic treatment with Metronidazole. This is because the probiotics help in decreasing the bacterial content and regulating the hydrogen and methane concentrations. Similarly, some gastroenterologist researchers also suggested that probiotics help in improving SIBO symptoms of diarrhea, constipation, bloating, and abdominal pain. However, probiotics are best effective for patients with both SIBO and IBS as compared to those with IBS without SIBO [4].

While treating SIBO with probiotics, there may be long-term and short-term approaches depending on the combination of a treatment plan prescribed to a patient.

Long-term approach

The long-term approach to treating SIBO with probiotics refers to the use of probiotics along with digestive support supplements, herbal antibiotics, fasting, or a restricted diet. This approach takes time of three to four days for the SIBO symptoms to be settled down, but this long-term approach is more effective and long-lasting with minimum chances of recurrence [5].

Short-term approach

The short-term approach of treating SIBO with probiotics refers to the use of probiotics along with the SIBO antibiotics where probiotics are considered as a secondary treatment intervention for SIBO. The most common and standard antibiotic prescribed for SIBO is Refaximin which helps in decreasing the bad bacteria in the small and large intestines. The success rate of Refaximin in treating SIBO and IBS is 67% when it is prescribed without probiotics, whereas when it is administered in combination with the probiotics, the success rate reaches 84%. This approach is called a short-term approach because it takes time of six to ten hours for the SIBO symptoms to be settled down after the administration of Refaximin and probiotics [3,5].

Concerns related to the Use of Probiotics for SIBO

Recent research claimed that the use of probiotics for SIBO is often coupled with some side effects such as brain fogginess, dizziness, and loss of appetite. This may be due to the growth of different bacteria i.e., other than Clostridium difficile, Escherichia coli, Klebsiella pneumonia, Enterococcus spp., and Proteus mirabilis, hence reacting differently as per the expected outcomes. Moreover, most of the probiotics are not prescribed by the physician as they are available over the counter and patients consume them without a medical prescription which can result in brain fogginess [6].

A well-reputed gastroenterologist described in detail the brain fogginess associated with the consumption of probiotics for inflammation and gut leakage associated with SIBO stating that the probiotics lead towards D-lactic acidosis in the small intestine due to which the level of endotoxins and cytokines in the blood is elevated than normal. These elevated endotoxins and cytokines cause inflammation in the brain causing brain fogginess [7].

Therefore, it is advised by gastroenterologists that probiotics should be consumed after a detailed and lab-based medical diagnosis of SIBO and under the extensive observation of a physician so that the side effects and the probiotic reaction could be monitored and addressed instantly.

Probiotics and Small Intestine Bacterial Overgrowth
Probiotics and Sibo


[1] Rao, S. S., Rehman, A., Yu, S., & De Andino, N. M. (2018). Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis. Clinical and translational gastroenterology, 9(6).

[2] Masjedizadeh, A. R., Alavinejad, P., & Shahinzadeh, S. (2020). Efficacy of Probiotics for Prevention of Small Intestinal Bacterial Overgrowth (SIBO) Recurrence among Patients with Irritable Bowel Syndrome (IBS). Afro-Egyptian Journal of Infectious and Endemic Diseases, 10(3), 279-286.

[3] Rao, S. S., & Bhagatwala, J. (2019). Small intestinal bacterial overgrowth: clinical features and therapeutic management. Clinical and translational gastroenterology, 10(10).

[4] Zhong, C., Qu, C., Wang, B., Liang, S., & Zeng, B. (2017). Probiotics for preventing and treating small intestinal bacterial overgrowth. Journal of clinical gastroenterology, 51(4), 300-311.

[5] Ruscio, D. (2020). SIBO, Probiotics, and Your Gut Health: A Long-Term Strategy. The Ruscio Institute for Functional Medicine. Available at:

[6] Wagner, N. R. F., Ramos, M. R. Z., de Oliveira Carlos, L., da Cruz, M. R. R., Taconeli, C. A., Branco Filho, A. J., ... & Campos, A. C. L. (2021). Effects of probiotics supplementation on gastrointestinal symptoms and SIBO after Roux-en-Y gastric bypass: a prospective, randomized, double-blind, placebo-controlled trial. Obesity Surgery, 31(1), 143-150.

[7] Rao, S. S., Yu, S., Tetangco, E. P., & Yan, Y. (2018). Probiotics can Cause D-Lactic Acidosis and Brain Fogginess: Reply to Quigley et al. Clinical and translational gastroenterology, 9, 1-2.


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