5 min|Dr. Maya Kuczma

SIBO Treatment: Beyond Diet Part 1

Wellness, Health, Gut Health

A Complex Treatment Plan For a Complex Problem

Small intestinal bacterial overgrowth (SIBO) is a complex problem; in most cases, a variety of risk factors have combined, over time, creating the ‘perfect storm’ for the development of SIBO. For this reason, no single treatment is completely effective at eradicating this condition.

It is best to approach SIBO with a complex treatment plan that addresses the root cause, as well as the bacterial overgrowth itself, including both dietary changes (SIBO Diet) and antimicrobial support, in addition to various supplements and lifestyle changes.


Prescription and Herbal

Since SIBO can be considered an infection based on the elevation of bacteria within the small intestine, initial research focused on the use of antibiotics. Today, antibiotics are still considered an important tool in the treatment of SIBO. However, since antibiotics are a common cause of SIBO, careful consideration must be taken to determine whether antibiotics are the best choice for treatment by weighing the cost and benefits of such a treatment.

Certain antibiotics are considered systemic. Their antibiotic or 'life-killing' properties take effect throughout the body, killing off valuable bacteria not only in the small intestine, but also in the other areas of the digestive tract, the vaginal canal, respiratory tract, skin, and elsewhere. In addition to the risk of systemic microbiome destruction, many antibiotics carry other risks such as the emergence of antibiotic-resistant organisms(1). Additionally, antibiotics alone do not necessarily address the root cause of SIBO and rates of recurrence are high, especially in cases of appendectomy, PPI usage, and older age(2).

However, certain antibiotics range from 50-91% effective in treating SIBO, depending on the antibiotic used and whether they were used in cases of methane or hydrogen dominant SIBO(3,4). A round of antibiotics typically lasts 7-10 days but may need to be repeated. In contrast, rounds of herbal antibiotics may last thirty days or more. Due to the high rates of efficacy, length of treatment, and personal preference, many doctors are utilizing specific antibiotics to treat SIBO.

Which Antibiotics Are Used to Treat SIBO?


Rifaxamin is the most commonly used antibiotic for treating SIBO. It is utilized in cases of hydrogen dominant SIBO, as well as with methane dominant SIBO in combination with neomycin(4,5). It is considered localized, staying within the gut rather than travelling throughout the body. It is effective both when used alone and in combination with neomycin(3,5).

It is also considered safe and provides additional benefits of modulating inflammation, reducing damage to the gut lining and hyperalgesia(6,7). Potential side effects include bloating, gas, abdominal pain, nausea, constipation, fatigue(8).


Neomycin is generally used only in cases of methane dominant SIBO alongside rifaxamin(5). It is poorly absorbed systemically, remaining in the gut where it is most active. Potential side effects include nausea, vomiting, and diarrhea(9).

Both Rifaxamin and Neomycin have been shown to be more active in the presence of bile salts(10,11). For this reason, it can be helpful to include supplements that promote bile flow or include bile salts alongside antibiotics, especially if gallbladder insufficiency is a concern.


Metronidazole is absorbed systemically and therefore affects the microbiome within the entire body. For this reason, many practitioners utilize rifaxamin and/or neomycin rather than prescribing metronidazole. However, metronidazole is more effective in the treatment of SIBO in patients with a blind-loop syndrome(12). Potential side effects include a headache, constipation, diarrhea, nausea, vomiting, cramping, and dry mouth(13).

Herbal Antibiotics

In a study comparing herbal antibiotic therapy to rifaxamin, herbals appear to be as effective as antibiotics, and effective in cases where patients did not respond to treatment with rifaxamin (14). In comparison with antibiotics, herbal antibiotics do not carry the same risk of resistance. Bacteria can change in order to adapt to antibiotics and resist their effects whereas herbal antibiotics consist of a wide variety of nutrients that work together, making it harder for bacteria to become resistant to their effects(15).

Herbal combinations such as Candibactin AR and BR, including multiple herbs such as barberry, oregano, thyme, yarrow, ginger, and coptis, are effective in treating SIBO and additionally provide anti-inflammatory, anti-viral, anti-biofilm, and immunomodulating effects (14,15). Many other herbs are utilized for the treatment of SIBO such as Neem, garlic, and goldenseal. However, even herbal antibiotics can affect healthy bacteria, and restoration of the microbiome may be required following treatment.

Additionally, herbal treatment typically lasts four weeks and may require multiple rounds, as well as rotation of various herbs and herbal combinations.Similarly to antibiotics, they alone may not address the root cause (The 9 Causes of SIBO That Has You Struggling).

Without additional treatment, bacteria can repopulate the small intestine within a couple weeks of completing herbal or prescription antibiotics. Addressing the underlying cause and staying on a maintenance diet can help to prevent recurrence.

Retesting follow antimicrobial treatment can also provide insight as to the efficacy of each round of antimicrobial therapy.In Part 2, we’ll explore additional treatment options to keep SIBO at bay (SIBO: Beyond Diet - Part 2).

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  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378521/
  2. https://www.nature.com/articles/ajg2008399
  3. https://www.ncbi.nlm.nih.gov/pubmed/20937045
  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691494/
  5. https://www.ncbi.nlm.nih.gov/pubmed/19996983
  6. http://onlinelibrary.wiley.com/doi/10.1111/apt.12735/full
  7. https://www.ncbi.nlm.nih.gov/pubmed/24161699
  8. https://www.rxlist.com/xifaxan-side-effects-drug-center.htm
  9. https://www.rxlist.com/neomycin-sulfate-side-effects-drug-center.htm
  10. https://www.nature.com/articles/182056a0
  11. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2934964/
  12. http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2036.2005.02397.x/full
  13. https://www.rxlist.com/flagyl-side-effects-drug-center.htm
  14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030608/
  15. https://www.sciencedirect.com/science/article/pii/S097594761630448X
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