A growing body of scientific evidence is challenging long-held assumptions about what threatens gut health, with new research suggesting that everyday industrial and agricultural chemicals may quietly disrupt the human microbiome in ways similar to antibiotics.
While antibiotics are widely known to wipe out both harmful and beneficial bacteria, scientists now say they are not the only substances capable of reshaping the gut ecosystem.
A major laboratory-based study has found that many common chemicals—originally designed to target insects, fungi or industrial materials—can significantly impair the growth and function of beneficial gut bacteria.
The research, conducted by scientists at the University of Cambridge and published in Nature Microbiology, examined how widespread synthetic chemicals affect the gut microbiome, which plays a crucial role in digestion, immune defence, metabolism and overall health.
Toxic chemical exposure has become nearly universal, with residues commonly found in food, drinking water and household environments. From nonstick cookware and flame-retardant furniture to pesticide-treated fruits and vegetables, these substances are deeply embedded in modern life.
Once inside the body, researchers say, many of these compounds interact directly with gut bacteria, disrupting microbial balance and potentially encouraging antibiotic resistance.
The Cambridge-led team tested 1,076 industrial and agricultural chemicals, including pesticides, plastic additives, flame retardants and chemical breakdown products commonly detected in food and water. These substances were exposed to 22 species of bacteria typically found in healthy human guts.
Rather than studying humans or animals, the researchers grew the bacteria in controlled laboratory conditions and observed how well they survived and multiplied when exposed to each chemical. A machine-learning model was then developed to predict which chemicals were most likely to harm gut bacteria.
The results were striking. Out of all the chemicals tested, 168 significantly slowed or completely stopped bacterial growth. Flame retardants such as tetrabromobisphenol A (TBBPA), commonly used in electronics and furniture, were found to substantially alter bacterial community structure.
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Several compounds—including closantel, an antiparasitic drug used in livestock; bisphenol AF, a plastic additive; and emamectin benzoate, an insecticide ingredient—caused broad-spectrum suppression, affecting multiple bacterial species at once.
In total, the researchers identified 588 harmful chemical-bacteria interactions, most of which were previously unknown. Notably, some of the most affected microbes were “keystone” species responsible for regulating inflammation and producing short-chain fatty acids such as butyrate, which nourish the cells lining the colon.
Indra Roux, Ph.D., of the University of Cambridge’s MRC Toxicology Unit and the study’s first author, said the findings were unexpected.
“We’ve found that many chemicals designed to act only on one type of target, say insects or fungi, also affect gut bacteria,” Roux said. “We were surprised that some of these chemicals had such strong effects. Many industrial chemicals like flame retardants and plasticizers—regularly encountered in daily life—weren’t thought to affect living organisms at all, but they do.”
One of the most concerning findings involved bacterial defence mechanisms. The study showed that some gut bacteria exposed to industrial chemicals activated efflux pumps—protein systems that expel toxic substances from cells. These same systems are commonly used by bacteria to resist antibiotics.
In several cases, bacteria that developed resistance to industrial chemicals also became more resistant to commonly used antibiotics. Researchers warn this suggests environmental pollution may be indirectly contributing to the global antibiotic resistance crisis by “training” bacteria to survive drug exposure even in the absence of antibiotics.
The study also found that chemical exposure altered bacterial metabolism. Some microbes survived by shutting down pathways responsible for producing beneficial compounds involved in immune regulation and cardiovascular health. While this helped the bacteria endure chemical stress, it reduced their ability to support human health.
Importantly, even low-level exposure was enough to trigger these changes. Researchers noted that small, routine exposures—such as pesticide residues on produce or flame-retardant particles in household dust—may be sufficient to disrupt the gut microbiome over time.
Scientists say the findings highlight a major blind spot in chemical safety regulation. Most safety assessments focus on whether substances harm humans directly, without considering their impact on the trillions of beneficial microbes living in the body.
“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,” said Kiran Patil, Ph.D., the study’s senior author.
He added that more real-world exposure data will be needed to determine how closely these laboratory findings reflect what happens in the human body.