Protocol development in integrative medicine is not typically a simple process. Individuals require individualized care, and what works for one patient may not work for another.

To establish these protocols, we first developed a Rating Scale that could be used to discern the rigor of evidence supporting a specific nutrient’s therapeutic effect.

The following protocols were developed using only A through C-quality evidence.

Qualifying studies
Minimum requirements
Systematic review or meta-analysis of human trials
RDBPC human trials
2+ studies and/or 1 study with 50 + subjects
RDBPC human trials
1 study

Small intestinal bacterial overgrowth (SIBO) occurs when there is an excessive amount of bacteria in the small intestine. In addition to the absolute number, the type of bacteria present in the small intestine can also impact the signs and symptoms a person may experience. (Dukowicz 2007) SIBO typically presents with digestive symptoms such as bloating, diarrhea, and abdominal pain. However, it may also manifest as skin conditions such as systemic sclerosis, psoriasis, and rosacea (Parodi 2008). Risk factors for SIBO include hypochlorhydria, motility disorders, irritable bowel syndrome, and medications such as proton pump inhibitors and histamine 2-receptor blockers. (Bures 2010)

While the gold standard of diagnosis is intestinal aspiration, breath tests using glucose or lactulose may also be used to test for hydrogen-dominant SIBO (H-SIBO) or methane-dominant SIBO (M-SIBO), with widely varying sensitivities and specificities. (Ghoshal 2017) Standard of care treatment for SIBO is antibiotics, though recurrence rates tend to be high; one study noted a 43.7% recurrence rate at 9 months post-antibiotic treatment. (Lauritano 2008)

SIBO is often found to be present with other comorbidities as well. For example, approximately one in four individuals with irritable bowel syndrome are commonly found to have SIBO as well. (Gandhi 2021)(Ghoshal 2020) And in those with functional dyspepsia (FD), a 2021 systematic review (SR) and meta-analysis (MA) found an increased risk of SIBO by 4.3x. (Gurusamy 2021) Of note, H. pylori is often present in FD, and its eradication may benefit FD. (Wang 2021)

There is a variety of therapeutics that may benefit either SIBO directly, related symptoms, or its frequent comorbidities. Certain probiotic strains may improve the efficacy of antibiotics and may have efficacy on their own. (Garcia-Collinot 2020) Herbal antimicrobials, such as cinnamon and others, were found in one study to be as effective as pharmaceutical antibiotics for SIBO eradication. (Chedid 2014) Finally, vitamin D tends to have beneficial effects on gastrointestinal flora. (Bashir 2016)

Based on current research findings, the ingredients in the protocol below have been associated with improved health outcomes in patients experiencing SIBO.


Two to four weeks of various strains, of perhaps Bifidobacterium strains or S. boulardii, at 5 billion CFU (colony forming units) (Garcia-Collinot 2020)(Kwak 2014)(Liang 2016)

  • 128 patients with gastrointestinal cancer and H-SIBO were treated with three strains of Bifidobacterium three times a day for four weeks. 81% of participants receiving probiotics, versus 25.4% of controls had eradication of SIBO. (Liang 2016)
  • 53 patients with chronic liver disease and H-SIBO were treated with the strains Bifidobacterium bifidum, Bifidobacterium lactis, Bifidobacterium longum, Lactobacillus acidophilus, Lactobacillus rhamnosus, and Streptococcus thermophilus. They were given 5 billion CFU of these probiotics twice a day for four weeks. Gastrointestinal symptoms improved in 24% of the probiotic group and worsened in 16% of the placebo group. (Kwak 2014)
  • 40 patients with SIBO and systemic sclerosis were assigned into three groups with antibiotics and/or probiotics twice per day for two months: metronidazole (M; 500mg), S. boulardii (P; 200mg), or metronidazole+S. Boulardii (M+P). At the conclusion of the study, eradication was achieved in 55% of the M+P group, 33% of the P group, and 25% of the M group. (Garcia-Collinot 2020)

View S. boulardii in the ingredient library

Probiotics in the Fullscript catalog

Anti-microbial herbs

Anti-microbial combination formulation, 2 times daily for minimum 4 weeks (Chedid 2014)

  • 104 participants treated with antibiotics or anti-microbial herbal therapy (2 capsules twice daily of Dysbiocide+FC Cidal or Candibactin-AR+Candibactin-BR) for four weeks experienced SIBO eradication in 34% and 46% of cases, respectively. Six cases of adverse effects were noted in the antibiotic groups, versus one case in the herbal therapy groups. (Chedid 2014) This study highlights the efficacy of herbs in the treatment of SIBO.
  • Additional antimicrobial herbs, such as cinnamon, may benefit individuals suffering from symptoms of SIBO such as chronic diarrhea. A 2019 MA found cinnamon to be effective for resolving chronic diarrhea (not necessarily in SIBO) in both adults and children. Effect sizes were unavailable due to study heterogeneity, and no serious adverse effects were reported. (Chen 2019)
  • Specifically, garlic may be an effective antimicrobial herb in SIBO due to its effects on H. pylori. H. pylori may act as a causative agent for SIBO, due to the pH-raising effects of the ammonia it produces. (Enko 2016) A 2019 SR and MA of 867 participants with H. pylori in eight RCTs found garlic to be an effective add-on therapy for H. pylori treatment. Dose tended to be 20 mg twice per day for three weeks. Garlic supplementation was found to improve H. pylori eradication rates, ulcer healing, and remission of symptoms. A significant risk of bias was noted in this review. (Si 2019)
Anti-microbial herbs in the Fullscript catalog

Peppermint oil

180 mg of enteric-coated capsules 2-3 times daily for 4-8 weeks (Cash 2016)(Merat 2010)(Cappello 2007)

  • Peppermint oil’s antispasmodic action can help reduce diarrhea and abdominal pain associated with irritable bowel syndrome (IBS). (Cash 2016)(Merat 2010)(Cappello 2007) Approximately 1 in 4 individuals with IBS also have SIBO. (Ghoshal 2020) As a result, peppermint oil supplementation may also help alleviate SIBO-related symptoms.
Peppermint oil in the Fullscript catalog

Vitamin D

140 IU of vitamin D3 per kg of body weight per day for 4 weeks followed by 70 IU per kg body weight for 4 weeks (Bashir 2016)

  • There is some evidence that SIBO may deplete vitamin D. A case report of a treatment-resistant bedsore and osteoporosis found vitamin D levels only began to rise after treatment of SIBO, despite two months of supplementation before SIBO treatment. (Kubota 2020)
  • In an open-label pilot study, 16 healthy participants were given 140IU/kg daily (to a maximum of 9800IU per day) of vitamin D for four weeks, followed by another four weeks of half of these doses. In the duodenum, decreases in the number of opportunistic bacteria, including H. pylori, were noted. No changes were noted in the ileum. (Bashir 2016)
  • Vitamin D tends to improve several different GI conditions, such as inflammatory bowel disease (IBD), by potentially improving gut dysbiosis, regulating immune responses to the gut microbiota, maintaining tolerance in the gut, and protecting the individual from IBD symptoms. (Shang 2017)

View Vitamin D in the ingredient library

Vitamin D in the Fullscript catalog


The Fullscript Integrative Medical Advisory team has developed these protocols to help health care practitioners make decisions when building treatment plans. By adding this protocol to your Fullscript template library, you understand and accept that the recommendations in the protocol are for initial guidance and may not be appropriate for every patient.

View template in-app
  1. Bashir, M., Prietl, B., Tauschmann, M., Mautner, S. I., Kump, P. K., Treiber, G., Wurm, P., Gorkiewicz, G., Högenauer, C., & Pieber, T. R. (2016). Effects of high doses of vitamin D3 on mucosa-associated gut microbiome vary between regions of the human gastrointestinal tract. European Journal of Nutrition, 55(4), 1479–1489. – D
  2. Bures, J., Cyrany, J., Kohoutova, D., Förstl, M., Rejchrt, S., Kvetina, J., Vorisek, V., & Kopacova, M. (2010). Small intestinal bacterial overgrowth syndrome. World Journal of Gastroenterology: WJG, 16(24), 2978–2990.  – F
  3. Cash, B. D., Epstein, M. S., & Shah, S. M. (2016). A Novel Delivery System of Peppermint Oil Is an Effective Therapy for Irritable Bowel Syndrome Symptoms. Digestive Diseases and Sciences, 61(2), 560–571. – B
  4. Cappello, G., Spezzaferro, M., Grossi, L., Manzoli, L., & Marzio, L. (2007). Peppermint oil (Mintoil) in the treatment of irritable bowel syndrome: a prospective double blind placebo-controlled randomized trial. Digestive and Liver Disease: Official Journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver, 39(6), 530–536. – B
  5. Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., Justino, E., Tomakin, E., & Mullin, G. E. (2014). Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Global Advances in Health and Medicine, 3(3), 16–24. – D
  6. Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & Hepatology, 3(2), 112–122. – F
  7. Enko, D., & Kriegshäuser, G. (2016). Helicobacter pylori infection and small intestinal bacterial overgrowth. Zeitschrift Fur Gastroenterologie, 54(05), P36.
  8. Gandhi, A., Shah, A., Jones, M. P., Koloski, N., Talley, N. J., Morrison, M., & Holtmann, G. (2021). Methane positive small intestinal bacterial overgrowth in inflammatory bowel disease and irritable bowel syndrome: A systematic review and meta-analysis. Gut Microbes, 13(1), 1933313. – A
  9. García-Collinot, G., Madrigal-Santillán, E. O., Martínez-Bencomo, M. A., Carranza-Muleiro, R. A., Jara, L. J., Vera-Lastra, O., Montes-Cortes, D. H., Medina, G., & Cruz-Domínguez, M. P. (2020). Effectiveness of Saccharomyces boulardii and Metronidazole for Small Intestinal Bacterial Overgrowth in Systemic Sclerosis. Digestive Diseases and Sciences, 65(4), 1134–1143.  – D
  10. Ghoshal, U. C., Shukla, R., & Ghoshal, U. (2017). Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy. Gut and Liver, 11(2), 196–208. – F
  11. Gurusamy, S. R., Shah, A., Talley, N. J., Koloski, N., Jones, M. P., Walker, M. M., Morrison, M., & Holtmann, G. (2021). Small Intestinal Bacterial Overgrowth in Functional Dyspepsia: A Systematic Review and Meta-Analysis. The American Journal of Gastroenterology, 116(5), 935–942. – A
  12. Kubota, Y., Nagano, H., Ishii, K., Kono, T., Kono, S., Akita, S., Mitsukawa, N., & Tanaka, T. (2020). Small intestinal bacterial overgrowth as a cause of protracted wound healing and vitamin D deficiency in a spinal cord injured patient with a sacral pressure sore: a case report. BMC Gastroenterology, 20(1), 283. – D
  13. Kwak, D. S., Jun, D. W., Seo, J. G., Chung, W. S., Park, S.-E., Lee, K. N., Khalid-Saeed, W., Lee, H. L., Lee, O. Y., Yoon, B. C., & Choi, H. S. (2014). Short-term probiotic therapy alleviates small intestinal bacterial overgrowth, but does not improve intestinal permeability in chronic liver disease. European Journal of Gastroenterology & Hepatology, 26(12), 1353–1359. – B
  14. Lauritano, E. C., Gabrielli, M., Scarpellini, E., Lupascu, A., Novi, M., Sottili, S., Vitale, G., Cesario, V., Serricchio, M., Cammarota, G., Gasbarrini, G., & Gasbarrini, A. (2008). Small intestinal bacterial overgrowth recurrence after antibiotic therapy. The American Journal of Gastroenterology, 103(8), 2031–2035. – D
  15. Liang, S., Xu, L., Zhang, D., & Wu, Z. (2016). Effect of probiotics on small intestinal bacterial overgrowth in patients with gastric and colorectal cancer. The Turkish Journal of Gastroenterology: The Official Journal of Turkish Society of Gastroenterology, 27(3), 227–232. – D
  16. Merat, S., Khalili, S., Mostajabi, P., Ghorbani, A., Ansari, R., & Malekzadeh, R. (2010). The effect of enteric-coated, delayed-release peppermint oil on irritable bowel syndrome. Digestive Diseases and Sciences, 55(5), 1385–1390. – B
  17. Parodi, A., Sessarego, M., Greco, A., Bazzica, M., Filaci, G., Setti, M., Savarino, E., Indiveri, F., Savarino, V., & Ghio, M. (2008). Small intestinal bacterial overgrowth in patients suffering from scleroderma: clinical effectiveness of its eradication. The American Journal of Gastroenterology, 103(5), 1257–1262. – D
  18. Shang, M., & Sun, J. (2017). Vitamin D/VDR, Probiotics, and Gastrointestinal Diseases. Current Medicinal Chemistry, 24(9), 876–887. – F
  19. Si, X.-B., Zhang, X.-M., Wang, S., Lan, Y., Zhang, S., & Huo, L.-Y. (2019). Allicin as add-on therapy for Helicobacter pylori infection: A systematic review and meta-analysis. World Journal of Gastroenterology: WJG, 25(39), 6025–6040. – A
  20. Wang, J., Gu, S., & Qin, B. (2021). Efficacy of Helicobacter pylori eradication therapy for treatment of functional dyspepsia: A protocol for systematic review and meta-analysis. Medicine, 100(20), e26045. – A