Supplements to Support Digestion and Prevent SIBO

There is a growing body of evidence suggesting that one of the major factors driving autoimmune disease is an excess of inflammatory bacteria in the small intestine. To control this overgrowth long-term, without harming our beneficial microbes, it is important to support the mechanisms that normally keep bacterial populations in check.

The Connection Between Stomach Acid, Enzymes, Bile, and Gut Bacteria

In contrast to the bustling ecosystem in the colon, the small intestine has a relatively low concentration of bacteria. This is a good thing since the walls of the small intestine are highly permeable to allow for nutrient absorption. We do not want a large population of bacteria in the small intestine, because their toxins would be too readily absorbed into the bloodstream.

Bacterial numbers are usually kept low in the small intestine by the combined effect of stomach acid, bile, and the rapid sweeping away of intestinal contents between meals. The small intestine actually goes through a “cleaning cycle” every couple of hours, but only when the stomach is empty. SIBO can occur when these usual mechanisms fail, whether the result of frequent snacking, acid-blocking medication, stomach acid or enzyme deficiency, celiac disease, hypothyroidism, scar tissue from abdominal surgery, or some other factor.

Adequate production of stomach acid, enzymes, and bile is essential to long-term control of SIBO and inflammatory gut bacteria. Bile, for example, directly suppresses many undesirable species, including Streptococci, Klebsiella, E.coli, and other bacteria that produce lipopolysaccharide.[i]  Digestive enzymes help prevent bacterial overgrowth in a different way­­—by ensuring rapid and efficient digestion, so that food does not remain in upper digestive system for too long.  Stomach acid is also important, because it helps to both break down food, directly suppress unwanted bacteria, and stimulate the flow of bile and digestive enzymes.

If any one of these three elements is lacking, bacterial overgrowth in the small intestine is likely to become a long-term problem.  It is unfortunately difficult to know whether you are already producing sufficient bile, acid, and enzymes, so some element of trial and error is needed when it comes to supplementing.

A stand-alone bile supplement is likely the best place to start, based on studies showing the ability of supplemental bile to improve psoriasis.[ii] Good options include:

The next step would be to add a supplement containing a combination of enzymes and betaine HCl (a source of hydrochloric acid). Here, the preferred choice is Thorne B.P.P.

This supplement contains betaine HCl, pepsin, and pancreatin. Pepsin is a powerful enzyme that breaks down protein in foods. Pancreatin is a combination of digestive enzymes (isolated from porcine pancreas) to break down fats, carbohydrates, and proteins. Pancreatin may be particularly useful if you are sensitive to starch, because it contains the enzyme amylase, which breaks down starch into simple sugars that can be more readily absorbed.

If you do not feel that you need to supplement with pancreatin, there are many other good digestive supplements that include only Betaine HCl and Pepsin, such as:

Pepsin and pancreatin-derived enzymes are preferable to “plant-based” enzymes, which are typically produced by culturing aspergillus mold on soy or barley. These fungal enzymes have a significant risk of contamination with mold toxins and gluten and are therefore best avoided.


Another useful strategy to control bacterial overgrowth in the long term and prevent SIBO from returning is to take a “prokinetic.”  Prokinetics are medications or supplements that can boost the natural cleansing process of the small intestine.  The preferred option is Iberogast, a European herbal tonic that has been used for decades and studied in countless clinical trials. (Ingredients include licorice, angelica, lemon balm, and chamomile).

Iberogast is an effective way to increase motility in the small intestine and bolster the digestive system’s housekeeping activity. [iii] It is best taken approximately 2 hours after eating. The typical dose is 20 drops, three times per day.

Alternatives to Iberogast include ginger and 5-HTP, both of which are found in the popular supplement MotilPro.  Many individuals battling SIBO report success with MotilPro, but there are some possible drawbacks.  Ginger may cause stomach upset, while long-term use of 5-HTP may potentially suppress important neurotransmitters, including dopamine and norepinephrine.[iv] (5-HTP stands for 5-hydroxytryptophan, which is a precursor to serotonin. Serotonin does boost small intestinal motility, which is why antidepressants are now a first line treatment for IBS.)

Other prescription options to increase motility are low-dose naltrexone and low-dose erythromycin.

The key to success with prokinetics is to keep using them long-term, to prevent SIBO from returning.



[i] Urdaneta, V., & Casadesús, J. (2017). interactions between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts. Frontiers in medicine4, 163.

Lorenzo‐Zúñiga, V., Bartoli, R., Planas, R., Hofmann, A. F., Viñado, B., Hagey, L. R., … & Gassull, M. A. (2003). Oral bile acids reduce bacterial overgrowth, bacterial translocation, and endotoxemia in cirrhotic rats. Hepatology37(3), 551-557.

[ii] Gyurcsovics, K., & Bertók, L. (2003). Pathophysiology of psoriasis: coping endotoxins with bile acid therapy. Pathophysiology10(1), 57-61.

Ely, P. H. (2018). Is psoriasis a bowel disease? Successful treatment with bile acids and bioflavonoids suggest it is. Clinics in Dermatology.

[iii] Madisch, A., Vinson, B. R., Abdel-Aziz, H., Kelber, O., Nieber, K., Kraft, K., & Storr, M. (2017). Modulation of gastrointestinal motility beyond metoclopramide and domperidone. Wiener Medizinische Wochenschrift167(7-8), 160-168.

[iv] Hinz, M., Stein, A., & Uncini, T. (2012). 5-HTP efficacy and contraindications. Neuropsychiatric disease and treatment, 8, 323.