Our understanding of the microbiome is constantly evolving. Frequently, there are new discoveries when it comes to taking care of our patients and their microbiota. To stay current with the latest microbiome research, functional medicine practitioners who prescribe probiotics need to consider some recent findings regarding their patients’ colonization patterns.


Microbiome Resistance

Recent research demonstrates that while mice have more static and indigenous features in their microbiome, human microbiomes are far more complex than we thought.1 Specifically, a small percentage of individuals have a degree of resistance to colonization that occurs when the intestinal microbiota protects itself against infiltration by some probiotic strains.

Due to genetic expression profiles and various other host features, probiotics are shown to transiently colonize these “resistant microbiome” patients differently, which clinically translates to affecting their unique microbiome signature, or lack thereof.1


The Unresponsive Patient

As a clinician in practice, you may have encountered a minor fraction of your patients who do not respond as well as you hoped to a daily probiotic regime. As described in the literature, the “resistant microbiome” nuance may be the reason.

For example, after several months of persistent symptoms and multiple stool tests, you may have concluded that the typical daily probiotic regimen for a select few patients is not gaining much traction and moving the clinical needle in the right direction as far as you expected, producing outcomes that are less than optimal.

While typical “permissive” patients would see positive effects in their microbiome with one probiotic strain blend, “resistant microbiome” patients may not show those much-desired results when given the same blend. However, they may be more “permissive” to a blend with different strains, which would produce more positive changes in their microbiome composition.2


The Bottom Line

We know the benefits of a daily probiotic are undeniable. When it comes to selecting a daily probiotic for healthy microbiome maintenance, a high-quality, broad-based, multi-strain/species blend with diverse representation across the phylogenetic tree continues to be the tried-and-true approach that works best for many patients.3

However, for the small minority of “resistant microbiome” cases, today’s functional medicine practitioners should have a complementary probiotic strain blend readily available to suit individual clinical needs for optimal gut health.





Joseph Ornelas, PhD, DC is the Pillars of GI Health Brand Manager at Lifestyle Matrix Resource Center. He holds a PhD from University of Illinois with concentration in Health Economics, an MA degree in Public Policy from the Harris School at the University of Chicago, an MS degree in Health Systems Management from Rush University, and a DC degree from National University of Health Sciences. As a licensed provider and health economist, Dr. Ornelas has published numerous evidence-based clinical practice guidelines, helping to improve quality standards of care and provide value for health care practitioners across several specialty areas.





1. Zmora N, Zilberman-Schapira G, Suez J, et al. Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell. 2018;174(6):1388-1405.e21. doi:10.1016/j.cell.2018.08.041

2. Wieërs G, Belkhir L, Enaud R, et al. How Probiotics Affect the Microbiota. Front Cell Infect Microbiol. 2020;9:454. Published 2020 Jan 15. doi:10.3389/fcimb.2019.00454

3. Khalesi S, Bellissimo N, Vandelanotte C, Williams S, Stanley D, Irwin C. A review of probiotic supplementation in healthy adults: helpful or hype?. Eur J Clin Nutr. 2019;73(1):24-37. doi:10.1038/s41430-018-0135-9