Elinav and his colleagues were surprised to see many healthy volunteers were actually resistant in that the probiotics couldn't colonise their GI tracts.
"This suggests that probiotics should not be universally given as a 'one-size-fits-all' supplement," he said.
"Instead, they could be tailored to the needs of each individual."
In the first of two studies, 25 human volunteers underwent upper endoscopies and colonoscopies to sample their baseline microbiome in regions of the gut.
Fifteen of those volunteers were then divided into two groups - the first group consuming generic probiotic strains, while the second being administered a placebo.
Both groups then underwent a second round of upper endoscopies and colonoscopies to assess their internal response before being followed for another two months.
The scientists discovered that the probiotics successfully colonised the GI tracts of some people, called the "persisters," while the gut microbiomes of "resisters" expelled them.
Moreover, the persister and resister patterns would determine whether probiotics, in a given person, would impact their indigenous microbiome and human gene expression.
The researchers could predict whether a person would be a persister or resister just by examining their baseline microbiome and gut gene expression profile.
They also found that stool only partially correlated with the microbiome functioning inside the body, so relying on stool as was done in previous studies for many years could be misleading.
In the second study, the researchers questioned whether patients should be taking probiotics to counter the effects of antibiotics, as they were often told to do in order to repopulate the gut microbiota after it's cleared by antibiotic treatment.
To look at this, 21 volunteers were given a course of antibiotics and then randomly assigned to one of three groups.
The first was a "watch-and-wait" group that let their microbiome recover on its own, while the second group was administered the same generic probiotics used in the first study.
A third group was treated with an autologous faecal microbiome transplant (aFMT) made up of their own bacteria that had been collected before giving them the antibiotic.
After the antibiotics had cleared the way, the standard probiotics could easily colonise the gut of everyone in the second group, but to the team's surprise, this probiotic colonisation prevented the host's normal microbiome and gut gene expression profile from returning to their normal state for months afterward.
In contrast, the aFMT resulted in the third group's native gut microbiome and gene program returning to normal within days.
"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 said.
"In contrast, replenishing the gut with one's own microbes is a personalised mother-nature-designed treatment that led to a full reversal of the antibiotics' effects."
Dr Olivier Gasser, translational immunology team leader at Wellington's Malaghan Institute of Medical Research, said antibiotic treatment created a "gaping hole" in the gut microbiome - an open niche that could very easily be colonised by good or bad bacteria.
"It is very important to close that hole as fast as possible, and if possible with a healthy set of bacteria," he said.
"That the research finds probiotics seem to inhibit this process is a very important finding."
Gasser said the new findings could signal the beginning of new legislation around probiotics.
"It's going to be interested to see how much effort is being put into recovering the patients' microbiome after antibiotics treatment," he said.
"I am not sure all health care providers are fully aware of the effects of antibiotics."
