A recent study led by the University of Cambridge has found that over 150 common industrial chemicals, including pesticides and flame retardants, are toxic to bacteria present in a healthy human gut microbiome. The research identified 168 chemicals that hinder the growth of beneficial gut bacteria, which play a key role in maintaining overall health.
The team tested 1,076 chemical contaminants on 22 different species of gut bacteria in laboratory conditions. Many of these chemicals, such as herbicides and insecticides used on food crops and substances found in plastics and flame retardants, were not previously believed to impact bacteria. Researchers noted that most of these chemicals likely enter the body through food, water, or environmental exposure.
Dr Indra Roux from 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.”
The researchers also observed that as gut bacteria attempt to resist these chemical pollutants, some develop resistance to antibiotics such as ciprofloxacin. This adaptation could potentially make certain infections more difficult to treat if it occurs within the human body.
Standard safety assessments for new chemicals typically do not consider their potential impact on the human gut microbiome because such substances are formulated for specific targets—for instance, insecticides are intended for insects.
To address this gap, the research team developed a machine learning model using their data set to predict whether current or future industrial chemicals may be harmful to human gut bacteria. The findings have been published in Nature Microbiology.
Professor Kiran Patil from the MRC Toxicology Unit at Cambridge and senior author 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 from Cambridge’s MRC Toxicology Unit added: “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.”
There is limited information available about how environmental chemicals directly affect the human gut microbiome and related health outcomes. Researchers suggest that people may regularly be exposed to these tested substances via daily life but acknowledge that actual concentrations reaching the gut remain unknown. More studies monitoring whole-body exposure will be needed to fully assess potential risks.
Patil commented: “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.”
As a precautionary measure until more is known about exposure levels and risks, researchers recommend washing fruits and vegetables before eating them and avoiding pesticide use in home gardens.
The research received funding from both the European Research Council (ERC) and 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