After analyzing the results, they found some of the guts hosted the probiotics, while others did not. “Persisters” experienced changes to their native microbiome and gut gene expression profile, but “resisters” did not.

» RELATED: Tips to prevent getting colds and flu, remedies

“Surprisingly, we saw that many healthy volunteers were actually resistant in that the probiotics couldn't colonize their GI tracts,” Elinav said. “This suggests that probiotics should not be universally given as a 'one-size-fits-all' supplement. Instead, they could be tailored to the needs of each individual.”

For the second part of the trial, the scientists wanted to explore whether probiotics have the ability to counter the adverse effects of antibiotics. Probiotics are supposed to repopulate the gut microbiota after it’s cleared by an antibiotic treatment.

They observed the guts of 21 volunteers by again administering upper endoscopies and colonoscopies after they were treated with antibiotics. The scientists either allowed the subject’s microbiome’s to repair on its own, with probiotics or an autologous fecal microbiome transplant made up of their own bacteria.

The scientists learned that the probiotics’ gut colonization prevented both the host gut’s gene expression and their microbiome from returning to their normal pre-antibiotic configurations months later.

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

Coauthor Eran Segal added, “This opens the door to diagnostics that would take us from an empiric universal consumption of probiotics, which appears useless in many cases, to one that is tailored to the individual and can be prescribed to different individuals based on their baseline features.”

» RELATED: Study suggests probiotics might boost weight loss in diet-based obesity