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The microbes in our guts could explain why people react differently to drugs, and lead to ways of making treatments work better.

We know that genetic differences can influence our response to drugs, but recent research has suggested that the microbial communities inside us could also help explain why some people experience toxic drug side effects when others don’t.

Most drugs are taken orally as pills. Often, these aren’t completely absorbed by the body, and the remains subsequently encounter enormous numbers of microbes in our guts.

To see what happens next, a team at Yale University and ETH Zurich in Switzerland mapped how 76 strains of human gut bacteria break down 271 pharmaceutical drugs.

They found that 176 were metabolised by at least one of the bacterial strains – a strikingly high proportion, says Michael Zimmermann at Yale University.

The study agrees with previous epidemiological research showing that microbes are key to how we metabolise drugs, says Tim Spector of King’s College London. “I think it’s a big step forward. People can start to predict, based on someone’s gut microbes, how they might respond to a drug.”

When microbes break down drugs, they may produce substances with unwanted side effects or that even render a drug’s active ingredient ineffective.

The finding that our gut bacteria may affect so many drugs hints at the possibility of changing our microbiomes to increase a drug’s efficacy or reduce side effects.

We may be able to do this through dietary changes or by more drastic measures such as a faecal transplant. The goal would be to change patients to suit their drugs, rather than the other way round.

The study mapped the interactions between different microbes and drugs by giving human bacteria to mice, so it is possible that the team’s findings won’t translate to humans.

“In drug metabolism, so many factors are involved,” says team member Maria Zimmermann-Kogadeeva, also of Yale University. “It is very hard to disentangle the microbe contribution from the human contribution because all the factors are happening at the same time.”