A large-scale laboratory screening of human-made chemicals has identified 168 chemicals that are toxic to bacteria found in the healthy human gut. These chemicals stifle the growth of gut bacteria thought to be vital for health.
Most of these chemicals, likely to enter our bodies through food, water, and environmental exposure, were not previously thought to have any effect on bacteria.
As the bacteria alter their function to try and resist the chemical pollutants, some also become resistant to antibiotics such as ciprofloxacin. If this happens in the human gut, it could make infections harder to treat.
The new research, led by the University of Cambridge, tested the effect of 1076 chemical contaminants on 22 species of gut bacteria in the lab.
Chemicals that have a toxic effect on gut bacteria include pesticides like herbicides and insecticides that are sprayed onto food crops, and industrial chemicals used in flame retardants and plastics.
The human gut microbiome is composed of around 4,500 different types of bacteria, all working to keep our body running smoothly. When the microbiome is knocked out of balance there can be wide-ranging effects on our health including digestive problems, obesity, and effects on our immune system and mental health.
Standard chemical safety assessments do not consider the human gut microbiome because chemicals are formulated to act on specific targets, for example insecticides should target insects.
The researchers have used their data to create a machine learning model to predict if industrial chemicals – whether already in use, or in development – will be harmful to human gut bacteria.
The research, including the new machine learning model, is published today in the journal Nature Microbiology.
Dr Indra Roux, a researcher at the University of Cambridge’s MRC Toxicology Unit and first author of the study said: “We’ve found that many chemicals designed to act only on one type of target, say insects or fungi, also affect gut bacteria. We were surprised that some of these chemicals had such strong effects. For example, many industrial chemicals like flame retardants and plasticisers – that we are regularly in contact with – weren’t thought to affect living organisms at all, but they do.”
Professor Kiran Patil in the University of Cambridge’s MRC Toxicology Unit and senior author of the study said: “The real power of this large-scale study is that we now have the data to predict the effects of new chemicals, with the aim of moving to a future where new chemicals are safe by design.”
Dr Stephan Kamrad at the University of Cambridge’s MRC Toxicology Unit, who was also involved in the study, said: “Safety assessments of new chemicals for human use must ensure they are also safe for our gut bacteria, which could be exposed to the chemicals through our food and water.”
Very little information is available about the direct effects of environmental chemicals on our gut microbiome, and in turn our health. The researchers say it’s likely our gut bacteria are regularly being exposed to the chemicals they tested, but the exact concentrations reaching the gut are unknown. Future studies monitoring our whole-body exposure will be needed to assess the risk.
Patil said: “Now we’ve started discovering these interactions in a laboratory setting it’s important to start collecting more real-world chemical exposure data, to see if there are similar effects in our bodies.”
In the meantime, the researchers suggest the best way to try and avoid exposure to chemical pollutants is to wash our fruit and vegetables before we eat them, and not to use pesticides in the garden.
This research was funded by the European Research Council (ERC) and the Medical Research Council UK (MRC).
Reference
Roux, I. & Lindell A. et al: ‘Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro.’ Nature Microbiology, November 2025. DOI: 10.1038/s41564-025-02182-6
Learn more about the research in Kiran Patil’s lab
A lab-based screening has discovered over 150 common industrial chemicals, from pesticides to flame retardants, that have a toxic effect on bacteria found in the healthy human gut microbiome. Some species of gut bacteria develop antibiotic resistance as they try to resist the effects of the chemicals.
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