Remission Cycle
The ultimate goal of SIBO treatment is long-term “remission”—meaning the excessive bacteria (or archaea) in the small intestine have been eliminated and the related symptoms have improved. Identifying the root cause of SIBO can ensure the best treatment, but remission is still possible even if the exact trigger remains unknown.
SIBO treatment begins with a “reset” phase, typically involving antibiotics or 2 weeks of elemental diet. Some individuals may require multiple treatment cycles before achieving lasting symptom relief. Once remission is reached, maintaining gut health through diet and lifestyle adjustments can help prevent or minimize future flare-ups.
It is very common for symptoms to return, especially in the early stages of SIBO treatment. Do not be discouraged. For many people SIBO remission can take time and multiple treatments. It is important to restart the treatment cycle and continue working toward regaining balance.
Treatment Options
Below, we outline evidence-based treatments designed to reduce the bacterial overgrowth responsible for SIBO.
Antibiotics
Antibiotics are a common first-line treatment for SIBO, with rifaximin (Xifaxan) being the most studied and widely used option. Antibiotics can successfully clear the small intestine of the overabundance of bacteria, reducing many digestive symptoms. (One caveat to note, is that antibiotics effectively work as a “nuclear” option, wherein they wipe out the “disrupter” bacteria but also your microbiome’s natural healthy bacteria. SIBO recurrence is also often high after antibiotic treatment as these medications often do not address the underlying causes for SIBO. Antibiotics can also cause gastrointestinal side effects, making a bad situation even worse. There is no standardized regimen of antibiotics due to the variability of bacteria involved. Some studies explore rotating antibiotic combinations to improve long-term outcomes, but further research is needed. In sum, antibiotics can provide quick, and relatively easy, symptom relief, but they can have unintended effects and do not address underlying causes, making relapse a significant concern.
Elemental Diet – An Emerging Treatment for SIBO
The Elemental Diet is one of the most effective treatments for SIBO, offering a non-pharmacological approach to reducing bacterial overgrowth. This liquid-based diet delivers nutrients in their simplest forms—amino acids, simple sugars, vitamins, and minerals—allowing them to be absorbed in the upper small intestine. This process deprives bacteria in the lower small intestine of their nutrient source, effectively starving the bacteria and leading to their eradication.
Despite its effectiveness, traditionally elemental diets have been difficult for patients to tolerate due to their truly bad taste. However, a 2023 clinical trial of a new palatable Elemental Diet (mBIOTA) achieved 100% patient compliance and showed an overall 73% eradication rate, with 83% of patients reporting symptom improvement. Currently only mBIOTA Elemental™ and Nestle's Vivonex Plus™ have undergone clinical trials to ensure treatment effectiveness for SIBO. Other semi-elemental products are available but none have been proven effective for treating SIBO and should be avoided.
Herbal Medicine
Some patients seek herbal alternatives for treating SIBO, though clinical research is limited. A retrospective study showed promising results, but prospective trials are lacking. While herbal antimicrobials may offer an alternative to antibiotics, their effectiveness and safety require further study before they can be considered reliable treatments.
Probiotics and Prebiotics – Not Recommended with SIBO
Probiotics
While probiotics are widely used for gut health, they may worsen SIBO symptoms. A 2018 study found that all patients experiencing brain fog were taking probiotics, with 50% testing positive for SIBO. Discontinuing probiotics and treating SIBO with antibiotics resolved their symptoms. Another study linked recent probiotic use to methane-positive SIBO, suggesting that probiotics may encourage bacterial overgrowth rather than resolve it. Probiotics should also be avoided while using an elemental diet as they work counter to its mechanism of action.
Prebiotics
Prebiotics, such as fiber, are generally not advised for SIBO patients. Since fiber is not digested by the gut itself, it becomes a food source for bacteria, leading to increased gas, bloating, and discomfort.
The physical structure of the gastrointestinal (GI) tract plays a crucial role in maintaining proper digestion and bacterial balance. Structural changes—whether congenital, disease-related, or caused by surgery—can slow motility, allowing bacteria to accumulate in the small intestine.