The Patil Group have published a paper in Nature Microbiology that reports the use of lab-based screening to identify over 150 common industrial chemicals, from pesticides to flame retardants, that have a toxic effect on bacteria found in the healthy human gut microbiome.
Very little information is available about the direct effects of environmental chemicals on our gut microbiome, and in turn our health. To address this the Patil Group, together with colleagues in Copenhagen, Washington, Düsseldorf and Tübingen, conducted a large-scale laboratory screen to test the effect of 1076 chemical contaminants on 22 species of gut bacteria.
They 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. The types of chemicals that had the greatest anti-gut bacterial activity were fungicides and industrial chemicals.
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.”
Using this data, Indra and colleagues created a machine learning model to predict if industrial chemicals - whether already in use, or in development - will be harmful to human gut bacteria.
Kiran Patil, Professor in the Department of Biochemistry 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.”
The study also found that 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.
Dr Stephan Kamrad, a corresponding author of 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.”
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).
Read the article: 'Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro', published in Nature Microbiology on the 26th November 2025.