Probiotics or "good bacteria," may not always be so good for you, according to a new pair of back-to-back studies. Researchers found that the gut could be resistant to standard probiotics in some cases, even delaying recovery in others.

Findings from the two studies were published in the journal Cell on September 6.

The presence of healthy bacteria (microbiome) in our gut not only improves digestion but is tied to our health and wellbeing as a whole. This is why many people take probiotics in the form of food as well as supplements.

And while probiotics generally receive a lot of support, experts still do not have a concrete understanding of them. Eran Elinav, one of the senior authors, notes that the relevant literature has remained very controversial.

He and his team wanted to find out if standard store-bought probiotics actually colonize our gastrointestinal (GI) tract and deliver the marketed health benefits. But unlike past studies which examined stool samples, the participants underwent upper endoscopy and colonoscopy — this allowed for a more accurate method of measuring gut colonization directly.

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

As per the study, some of us may be "persisters," meaning the probiotics are successful in colonizing our guts. But chances are you might be among the "resisters," whose guts end up expelling probiotics.

Now, the next question was whether these probiotics facilitate recovery in patients who have taken antibiotics. Antibiotic treatment is a double-edged sword since it kills both good bacteria and bad bacteria.

The second study dived into this by examining 21 volunteers who had taken antibiotics, dividing them into three groups. The first group did not intervene and allowed their gut microbiome to recover on its own. The second group was given probiotics, the same kind used in the first study. The third group was administered their own bacteria, which was collected before they had taken the antibiotics.

Surprisingly, probiotic use actually seemed to delay recovery in the second group. The normal microbiome and gut gene expression profile of the people in this group did not return to a normal state for months, the researchers found.

"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 stated.

In contrast, the third group was able to make a swift recovery within days, he added. This suggested that a "personalized mother-nature-designed treatment" by using one's own microbes could successfully reverse the effects of the antibiotics.