Before the advent of the probiotics market, the concept of spending money on bacteria and intentionally swallowing it probably puzzled a lot of people. Today, the practice has become normalized: Supplements, yogurts, and other probiotic dietary products tout the benefits of “good” bacteria in the gut flora, especially in terms of replenishing the digestive tract following the harsh effects of an oral antibiotic treatment, which can wipe out beneficial bacteria in the gut.

Now, two new studies are providing some evidence that use of probiotics is still not well-understood, and may not be as helpful to the body as many consumers have been led to believe. For some, they may have no effect at all. For others, the reaction could be potentially harmful.

For papers published in the journal Cell, researchers at the Weizmann Institute of Science and the Tel Aviv Medical Center in Tel Aviv, Israel conducted two investigations that examined how the body responds to ingestion of probiotic supplements. In the first study, 15 subjects consented to two endoscopic procedures, with physicians performing an endoscopy (in which a device is fed to the stomach through the throat) and colonoscopy (the endoscope is inserted rectally and into the large intestine) to retrieve samples. The subjects were then split into two groups. One group of 10 took commercially available probiotics, while the remaining five took a placebo. After two months and two follow-ups, researchers found that four of the 10 study subjects simply expelled the probiotics. Dubbed “resisters,” they failed to hold on to the bacteria. The six others, dubbed “persisters,” successfully retained the bacteria and colonized it in their guts. This demonstrates that not everyone who takes a catch-all type of probiotic is able to assimilate the product in their digestive tract.

In the second study, researchers looked at whether probiotics could re-colonize intestinal flora that had been damaged by a course of antibiotics, which typically apply a scorched-earth approach to bacteria in the body. A total of 21 subjects were split into three groups, with one taking nothing after antibiotics, one taking conventional probiotics, and one receiving a fecal transplant to mimic the original bacterial make-up in the gut prior to antibiotic use. (In a fecal transplant, feces are inserted throughout the colon to repopulate beneficial bacteria. In this case, patients received their own stool collected prior to taking the antibiotics.)

The group that did nothing restored their normal flora in time. Those who received a fecal transplant returned to their baseline flora almost immediately. Those who took probiotics saw their systems populated by the new bacteria, but it hindered their normal flora from flourishing.

There are several caveats to this research that bear mentioning. First, the sample size for both studies was small. There’s also no clear answer as to the potential consequences of pre-formulated probiotics taking over “normal” gut flora and whether a failure to return to baseline carries any health consequences. While restoring normal flora is desirable, fecal transplants are not a widely used treatment and are typically reserved only for cases of severe complications from antibiotic use or certain other ailments. People with chronic digestive issues (such as inflammatory bowel disease or Crohn’s disease) were not included. Finally, the study did not examine the consequences of probiotic use in conjunction with antibiotic use and whether it may act as a preventative measure to maintain rather than restore bacteria during a course of treatment.

Importantly, researchers found a discernible difference between the so-called persisters and resisters, with a portion of subjects in the first study having no reaction to the administered probiotics. The findings demonstrate that one approach may not fit all—and before taking any probiotic supplements yourself, it's best to consult a physician.