How medicines affect gut bacteria could inform safer, more effective use, says new study

Some everyday medicines – not just antibiotics – could influence gut bacteria in ways that affect how other treatments work, according to a new review by the Medicines and Healthcare products Regulatory Agency (MHRA) and University of Glasgow. The findings open up opportunities to better tailor treatments to individuals and improve how medicines are used together in real life. 

The review, published today (23 December) in Nature npj Antimicrobials and Resistance by Shirley Do Nascimento and colleagues, brings together evidence that a wide range of drugs – including diabetes treatments and antipsychotics – can change the make-up of the trillions of bacteria in our gut that keep us healthy. These subtle changes could play a role in how medicines work in the body, particularly when treatments are taken together. 

Understanding how drugs interact with gut bacteria could help researchers and the MHRA build on the strong existing evidence base around medicine safety, better understand why some people respond differently to the same medicine, and support the development of treatments that are even safer and more effective over time.  

Dr Chrysi Sergaki, senior author of the study and Head of Microbiome at the MHRA, said: 

“Antibiotics are well known to affect gut bacteria, but this review shows that some other common medicines can also influence the microbiome. Building this understanding helps us identify where better data could improve drug development and, ultimately, patient care – while also supporting the responsible use of antibiotics. 

“These findings could help researchers understand why some patients respond differently to the same treatment, and why certain side effects occur in some people but not others.”  

The gut microbiome – the community of trillions of bacteria that live in the digestive system – plays a key role in immunity and metabolism. While the effects of antibiotics on this balance are well established, the review highlights evidence that several non-antibiotic medicines may have similar, if more subtle, effects.  

For example, the review highlights that: 

• Metformin, a widely used diabetes medicine, alters gut bacteria in ways that may contribute to both its benefits and some side effects, such as bloating or diarrhoea. 

• Antipsychotic medicines have been shown in studies to disrupt gut bacteria linked to weight gain and metabolic changes. 

Better understanding of how medicines affect gut bacteria could also support efforts to protect the effectiveness of treatments, including antibiotics. The gut is a major home for bacteria and other microorganisms, including those carrying resistance genes. When the balance of gut bacteria is disrupted, resistant bacteria can gain an advantage. Identifying medicines that are less disruptive to the microbiome could, over time, help slow the spread of antimicrobial resistance. 

Dr Anastasia Theodosiou, co-author of the paper at the University of Glasgow, said: 

“This paper is an important step towards recognising the microbiome as something we need to protect – and towards designing and testing medicines that are not only more effective, but also safer for our microbiomes.” 

The MHRA is working with researchers and innovators to develop updated standards for studying how medicines affect the gut microbiome – and other microbiomes, such as the vaginal microbiome – during drug development, where appropriate. The aim is to build consistent, reliable evidence that can be used by regulators and developers alike. 

The MHRA is also exploring new ways to improve how side effects and interactions between medicines are predicted. This includes: 

• The Yellow Card Biobank, which links reports of suspected side effects to genetic and biological data, helping researchers better understand why some people experience adverse reactions. 

• A new study using AI and anonymised NHS data to predict potential side effects from combinations of medicines before they reach patients is particularly important as millions of people in the UK take multiple medicines, and some interactions can lead to avoidable side effects, extra GP visits or hospital stays.  

The long-term goal is to develop tools that help doctors understand how combinations of medicines affect people in real life, supporting safer, more effective prescribing that can be more closely tailored to individual patients. 

Patients should keep taking their medicines as prescribed. Do not stop or alter your treatment without speaking to a healthcare professional. If you have any concerns or questions, seek advice from your doctor or pharmacist, and report any suspected side effects via the Yellow Card scheme.    

Notes to editors  

1. Publication: S. Do Nascimento et al. (2025) ‘Microbiotoxicity: An under-recognised player in drug efficacy, toxicity, and health outcomes' Nature npj Antimicrobials and Resistance. DOI: 10.1038/s44259-025-00165-5. 

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