Good Gut Bacteria are Being Affected by Common Drugs

One in every four drugs can affect good gut bacteria with their side effects, finds a new study. These drugs can also cause antibiotic-like side-effects on the gut bacteria.

One in every four drugs can affect the growth of good gut bacteria. These drugs result in antibiotic-like side-effects and may promote antibiotic resistance, finds a new study. The findings of this study are published in the Nature journal.

The research team screened over 1000 marketed drugs against 40 representative bacteria from the human gut and found that more than a quarter of the non-antibiotics (250 out of 923) affect the growth of at least one species in the microbiome. EMBL group leaders Peer Bork, Kiran Patil, Nassos Typas, and Georg Zeller led the work.

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‘A surprisingly huge number of unrelated drugs can affect the gut bacteria negatively. They can even change the gut microbiome composition. This change in the composition of gut bacteria can contribute to bad digestive health.’

Widespread phenomenon

The human gut contains a large number of species of bacteria, collectively referred to as the gut microbiome. In the last decade, it has become clear that the composition of the gut microbiome affects human health. It is well-known that antibiotics have a large impact on this microbiome, for example causing gastrointestinal side effects.

Recently, a few commonly used non-antibiotic drugs have been shown to cause changes in gut microbiome composition, but the full extent of this phenomenon was unknown until now. The current paper is the first to systematically profile direct interactions between marketed drugs and individual gut bacteria. Not only anti-infectives but drugs from all therapeutic classes inhibited the growth of different gut microbes.

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"The number of unrelated drugs that hit gut microbes as collateral damage was surprising," says Peer Bork. "Especially since we show that the actual number is likely to be even higher. This shift in the composition of our gut bacteria contributes to drug side-effects, but might also be part of the drugs' beneficial action."

Kiran Patil adds: "This is just the beginning. We don't know yet how most of these drugs target microbes, how these effects manifest in the human host, and what the clinical outcomes are. We need to carefully study these relationships, as this knowledge could dramatically improve our understanding and the efficacy of existing drugs."

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Unnoticed risks

The study also highlights the previously unnoticed risk that consumption of non-antibiotic drugs may promote antimicrobial resistance, as the general resistance mechanisms of microbes to human-targeted drugs and to antibiotics seem to largely overlap.

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"This is scary," says Nassos Typas, "considering that we take many non-antibiotic drugs in our life, often for long periods. Still, not all drugs will impact gut bacteria and not all resistance will be common. In some cases, resistance to specific non-antibiotics will trigger sensitivity to specific antibiotics, opening paths for designing optimal drug combinations."

Personalised medicine

"We are excited to move on and explore drug-microbe interactions in complex gut microbial communities, as this will help us understand how individuals sometimes respond differently to the same medication," says Georg Zeller. Each of us harbors a unique gut microbiome. We all carry different bacterial species - besides several common ones - and on top of that, we carry different individuals of the same species called strains. These strains can have very different functionalities, including the response to drugs. Therefore, many drug-microbe interactions are likely to be individual, opening paths for personalized drug therapies aimed at the individual gut microbiome.

Source-Eurekalert