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https://www.science.org/content/article/pesticides-may-wreak-havoc-gut-microbiomeVelmurugan Ganesan of the KMCH Research Foundation wondered whether pesticide exposure could explain a curious finding. In a study of almost 3000 people in southern India, his team found that 23% of participants in urban areas had diabetes, which clustered with classic risk factors such as obesity and high cholesterol. Yet in rural areas, the prevalence was still 16%, and there was no association with those risk factors. “We started wondering whether environmental chemicals could be playing a role,” Ganesan says.
The team then explored the effects of exposure to one widely used agricultural insecticide, chlorpyrifos, in mice. Previous animal studies had often tested high doses for short periods, but Ganesan’s team used what he calls a “realistic dose,” based on pesticide residues in the average Indian diet, for 120 days. The study, published in August 2025, found that chlorpyrifos reshaped the gut microbiome, with beneficial bacteria such as Lactobacillus declining and potentially harmful species such as Helicobacter rising. Mice exposed to chlorpyrifos also developed high blood sugar and diabetes, despite not gaining weight, says Karthika Durairaj, the study’s first author.
Another study co-authored by Ganesan suggests a possible mechanism: When gut microbes break down chlorpyrifos, they produce acetate and other metabolites the liver uses to make glucose through a process called gluconeogenesis, leading to elevated blood sugar levels.
Ganesan’s team is now analyzing blood, urine, and stool samples from people with diabetes, both with and without obesity, and healthy controls to examine whether the patterns hold up in humans. “We are working to show that diabetes induced by environmental chemicals is quite different [from lifestyle-associated diabetes] in its underlying disease mechanisms and could require different clinical care,” Ganesan says.
Pesticides appear to drive not just population shifts in the microbes, but also changes in their activity. In a large study published in 2025, for example, researchers exposed 17 representative bacterial species from the human gut to 18 different pesticides and detected changes in the microbial production of hundreds of small molecules. They included short-chain fatty acids, bile acids, and tryptophan-related molecules—compounds that help keep the gut lining healthy, regulate inflammation, and guide immune responses.
“Most studies focus on the effect of pesticides on … gut microbial composition, but this study shows that effects are far greater than that,” says study co-author Caroline Johnson, an environmental health epidemiologist at the Yale School of Public Health. The team also found that some bacteria accumulate pesticides within their cells, which could prolong their presence in the human body and increase the risk of long-term health effects.