Repopulating the Gut with Probiotics

IFM’s Advanced Practice Modules (APM) offer insight into a range of clinical conundrums and provide useful clinical pearls on approaching care through the functional medicine lens. Below is a question that is frequently asked by attendees during the Immune program. 

If probiotic supplements are just transient visitors, how do you repopulate the gut?
Probiotics can help shift the balance of the gut microbiome from less beneficial and potentially pathogenic organisms to commensal and beneficial species. Probiotics also modulate the immune response, decreasing intestinal inflammation and preventing infection.1 Their presence can be maintained through the use of prebiotics in food or supplements.2,3 Prebiotics feed gut microbes and help encourage colonization and biofilm production. If probiotics are administered without additional dietary modifications, the impact on probiotic administration from a therapeutic perspective may be limited. It is important to note that consumption of probiotic-containing foods such as kimchi, sauerkraut, kefir, and kombucha can help encourage symbiotic and commensal organisms to maintain a long-term presence. 

Clinical takeaway: Although probiotics are transient visitors, they play a role in shifting the overall balance of the microbiome, modulating the immune system, and decreasing inflammation. To maintain that benefit, probiotics need to be generally consumed long-term. Consuming probiotics in foods as well as prebiotic foods or supplements can encourage colonization of commensal organisms over time.

Probiotics help support immune system balance and may be an effective treatment for some autoimmune conditions. At the upcoming Immune Advanced Practice Module (APM), clinicians will explore connections between gut health, inflammation, and immunity.

Learn More About Immune Imbalance


  1. Gagliardi A, Totino V, Cacciotti F, et al. Rebuilding the gut microbiota ecosystem. Int J Environ Res Public Health. 2018;15(8):1679. doi:10.3390/ijerph15081679
  2. Korpela K, Salonen A, Vepsäläinen O, et al. Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants. Microbiome. 2018;6(1):182. doi:10.1186/s40168-018-0567-4
  3. Makki K, Deehan EC, Walter J, Bäckhed F. The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe. 2018;23(6):705-715. doi:10.1016/j.chom.2018.05.012