Bacteria in probiotics can evolve in your gut and turn nasty, study shows

The “good bacteria” in probiotic drinks and remedies can evolve in the body and have the potential to become harmful, according to a study which calls for caution in the emerging field of treatment.

Researchers from the University of Washington, Missouri, have shown how one strain of bacteria sold in Europe in an anti-diarrhoea probiotic can begin to attack the protective coating of the intestine.

This is one factor that can increase the risk of conditions like irritable bowel syndrome (IBS) and other probiotics have been linked to serious infections in some people.

In trials on mice the researchers showed that high fat and sugar diets, antibiotic use and the other bacteria in the gut all boosted this unpredictable probiotic evolution.

“Probiotics are fundamentally different from other drugs because they can evolve during treatment,” Dr Guatam Dantas, a microbiologist who lead the study published in Cell Host and Microbe on Tuesday.

“This isn’t a reason not to develop probiotic-based therapies, but it is a reason to make sure we understand how they change and under what conditions.”

Increasing recognition of the complex role the ecosystem in our digestive tract has on everything from weight, to diabetes, and our mental health has sparked a wave of new research on probiotics.

This is now leading to treatments beyond the daily yoghurt drinks like Yakult – which claim “good” bacteria promote general gut wellbeing – into targeted treatments for metabolic conditions like IBS and phenylketonuria, a disorder that causes nerve damage.

But approving conventional treatments relies on being able to predict everything from their effects, chances of harm and how long they will last- which makes understanding how bacteria change vital.

For their research, Dr Dantas and colleagues studied a probiotic from the E coli bacteria, known as E coli Nissle, which was first isolated in 1917 from a First World War soldier who emerged unscathed from a diarrhoea outbreak.

They tested how E coli Nissle changed in mice with normal and depleted microbiomes, pre and post-antibiotic treatment. The bacteria was also tested on an array of diets designed to mimic different levels of fibre – which promotes gut bacteria diversity – or a junk food “western diet”, which depletes them.

In healthy normal mice they did not see much change in the E coli Nissle bacteria probiotic.

“But you have to remember that quite often we wouldn’t be using probiotics in people with a healthy microbiome,” said Aura Ferreiro, first author of the study.

“We would be using them in sick people who have a low diversity, unhealthy microbiome. And that seems to be the condition when the probiotic is most likely to evolve.”

Using their findings they were able to engineer a new probiotic which did not evolve and which could help treat patients with phenylketonuria, by breaking down chemicals in diet that they cannot digest naturally.

This shows that the same principles can be used to design safer probiotics, but equally that future treatments need larger widespread testing, the study concluded.