Probiotic Resistance

Last night, I caught a podcast from CBC on Quirks & Quarks. The 15 minute podcast is on the page linked. There are two papers linked

There are several highlights:

  • The murine (mouse) & human gut mucosal microbiome only partially correlates with stool
  • Mice feature an indigenous-microbiome driven colonization resistance to probiotics
  • Humans feature a person-specific gut mucosal colonization resistance to probiotics
  • Probiotic colonization is predictable by pre-treatment microbiome & host features
  • Murine gut mucosal probiotic colonization is only mildly enhanced by antibiotics
  • Human gut mucosal probiotic colonization is significantly enhanced by antibiotics
  • Post antibiotics, probiotics delay gut microbiome and transcriptome reconstitution
  • In contrast, aFMT restores mucosal microbiome and gut transcriptome reconstitution


Some quotes from reviews:

“”Although all of our probiotic-consuming volunteers showed probiotics in their stool, only some of them showed them in their gut, which is where they need to be,” says Segal.

They also found that stool only partially correlates with the microbiome functioning inside the body, so relying on stool as was done in previous studies for many years could be misleading.

“Contrary to the current dogma that probiotics are harmless and benefit everyone, these results reveal a new potential adverse side effect of probiotic use with antibiotics that might even bring long-term consequences,” Elinav says. ” [src]

“While probiotics are viewed as safe for healthy individuals, potential harms may be underreported: a recent systematic review of randomized controlled trials of probiotics, prebiotics or synbiotics showed that only nine of 384 trials (2 percent) appropriately reported harms according to guidelines outlined in the CONSORT (Consolidated Standards of Reporting Trials) Statement. Further, the long-term impact of taking probiotics has not been systematically investigated.

In the participants where probiotic strains could be detected, yes, there was a detectable change in their gut microbiome. However, there was no predictability or consistency in the change to the microbiome.” [src]

“Elinav’s group found that six of the treated subjects had higher levels of colonization with the probiotic microbes, whereas the other four remained the same as their baseline….Just by looking at stool samples, the researchers could not differentiate between the two groups—the responders and the nonresponders—corroborating their earlier findings that stool samples may not always reflect what is happening inside the gut. ” [src]

Bottom Line

These papers help clarify that trying probiotics is around a coin-toss in terms of probability. In my humble opinion, non-antibiotic and non-probiotic intervention is looking more and more a better path. It may also be slower, but the changes are more likely to persist.

This recent study, also in Cell, help illustrates the point of diet impacting the microbiome.


My analysis site has the current evidence base interactions between a vast number of substances and the microbiome.