Drinking probiotics might not bring benefits Silke Weinsheimer/Getty

Probiotics are living micro-organisms that are taken by millions of people to boost their microbiome or to restore their gut ecosystem after a dose of antibiotics. Yet questions remain about whether they actually work.

To find out what really goes on in the gut when people ingest probiotics, immunologist Eran Elinav of the Weizmann Institute of Science in Israel, and colleagues, sampled the microbiome of healthy volunteers directly using endoscopies and colonoscopies. Most other microbiome research relies on faecal samples as a proxy for gut microbes.

They then fed 15 of the volunteers either a commercially available probiotic supplement or a placebo.


The outcome was striking. For a start, the microbes found in faeces were not representative of those that had colonised the gut. “Relying on faecal samples as an indicator of what goes on inside the gut is inaccurate and wrong” says Elinav.

The research also showed that while probiotics colonised the gastrointestinal tract of some people, the gut microbiome of others just expelled them. There was no way of telling from their stool sample which category people fell into. “Some people accept probiotics in their gut, while others just pass them from one end to the other,” says Elinav. They found that the probiotic colonisation patterns were highly dependent on the individual. That tells us that the concept that everyone can benefit from a universal probiotic bought from the supermarket is empirically wrong, he says.

Potent disturbance

Next the researchers measured what happens to the microbiome of people who take probiotics in the hope of restoring their microbiome after antibiotics. Twenty-one volunteers took an identical course of antibiotics and were then assigned to one of three groups. The microbiome of the first group was allowed to recover by itself, whereas the second group was given probiotics. The third group was treated with a dose of their own original pre-antibiotic microbiome by a faecal microbiota transplant (FMT).

Probiotic bacteria readily colonised the gut of everyone in the second group after antibiotics had cleared the way. However, the researchers were surprised to find that this prevented the return of the person’s normal microbiome for up to six months. “The probiotics very potently and persistently prevented the original microbiome returning to its original situation,” says Elinav. “This was very surprising and alarming to us. This adverse effect has not been described to date.”

The opposite effect was observed with the patients given a dose of their own pre-antibiotic microbiome via FMT. Their native gut microbiome returned to normal within days.

Although the researchers did not measure the clinical impact of the prolonged microbiome disturbance, previous studies have found a link between disruption to gut microbes and obesity, allergies and inflammation. “It’s potentially harmful,” says Elinav.

The take-home message is that probiotics don’t always live up to their harmless reputation, and to be effective, their formula needs to be tailored to the individual.

Journal reference: Cell, DOI: 10.1016/j.cell.2018.08.041; 10.1016/j.cell.2018.08.047