Researchers at the University of Cambridge have found that 168 common industrial and agricultural chemicals can harm beneficial bacteria in the human gut, with some also promoting resistance to antibiotics. Drawing on a large laboratory screen, the team created a machine learning model to predict which chemicals may pose risks to the microbiome.
A large-scale laboratory study led by the University of Cambridge's MRC Toxicology Unit tested 1,076 human‑made chemical contaminants on 22 species of gut bacteria. The researchers identified 168 substances that interfered with the growth of microbes typically found in a healthy human gut, including pesticides such as herbicides and insecticides used on crops, as well as industrial chemicals found in flame retardants and plastics.
According to the University of Cambridge and affiliated press coverage, many of these chemicals are likely to enter the body through food, drinking water or general environmental exposure, yet most were not previously believed to affect bacteria. The substances identified as harmful stifled the growth of gut bacteria thought to be important for health.
The human gut microbiome is estimated to contain about 4,500 different types of bacteria that collectively support digestion, weight regulation, immune function and aspects of mental health. When this community becomes imbalanced, it has been linked to problems such as digestive disorders, obesity, immune conditions and mental health issues.
In the new work, the researchers observed that as gut bacteria adapted to some of the tested chemicals, certain species developed resistance to antibiotics such as ciprofloxacin. If similar processes occur in the human body, this could make some infections harder to treat, they cautioned.
Standard chemical safety assessments generally do not account for effects on the gut microbiome, in part because many substances are formulated to act on specific targets, such as insects in the case of insecticides, rather than on humans or their resident microbes.
Using the data from their screening experiments, the team developed a machine learning model to predict whether existing or newly designed industrial and agricultural chemicals are likely to harm human gut bacteria. The study, "Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro," was published in Nature Microbiology (2025; 10(12): 3107).
Dr. Indra Roux, first author of the study and a researcher at the MRC Toxicology Unit, said in a University of Cambridge release: "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 plasticizers -- that we are regularly in contact with -- weren't thought to affect living organisms at all, but they do."
Professor Kiran Patil, senior author of the study at the same unit, 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, another member of the research team, 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."
The scientists stressed that there is still limited information on how environmental chemicals directly influence the gut microbiome and human health in real‑world conditions. While the laboratory data suggest that gut bacteria are likely to encounter many of the chemicals tested, the actual levels reaching the gut in everyday life remain unclear. Future research that tracks overall chemical exposure in the body will be needed to determine the true risks.
Patil noted: "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, Cambridge researchers and associated health guidance suggest practical steps to reduce exposure to chemical pollutants, such as washing fruit and vegetables thoroughly before eating and avoiding the use of pesticides in home gardens.
