Industrial chemicals in our food and water are reshaping our gut microbiomes

By Julia RiesFact-checked by Barbara BekieszPublished January 12, 2026


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If common environmental chemicals suppress certain beneficial bacteria or shift the balance of species, that can plausibly change inflammation, metabolic signaling, and immune responses.

—Thushara Galbadage, MD, PhD

Scientists have long known that chemicals spill into our food and water sources, contaminating the food we eat and beverages we drink.

A new report, published in Nature Microbiology, adds to growing evidence that these chemicals can harm human health. []

After examining the effects of various pollutants, the researchers discovered a number of pesticides and fungicides that may inhibit the growth of gut bacteria and alter the microbiome—the community of microorganisms that resides in our guts. []

Related: The 3 most toxic chemicals found in our food and water

How do these chemicals get into the food we eat?

There are multiple routes, according to Don Thushara Galbadage, MD, PhD, a public health professor at Texas Christian University whose research focuses on microbiology and infectious disease pathogenesis.

For example, pesticides sprayed onto crops, and pollutants from nearby industrial facilities and wastewater sources, can travel and contaminate farms, he explains.

In addition, materials used in food manufacturing facilities—such as plastic—may leach chemicals. Finally, pollutants in our seawater and feed can accumulate in the animals we consume.

Scientists are still learning about how these chemicals affect the gut microbiome—and how those changes might impact human health. 

The microbiome plays a role in a number of bodily functions: It supports the immune system, fights pathogens, and aids digestion. []

“If common environmental chemicals suppress certain beneficial bacteria or shift the balance of species, that can plausibly change inflammation, metabolic signaling, and immune responses,” says Dr. Galbadage. Traditional toxicity testing, which looks for damage in the kidney or liver, wouldn’t pick up on these effects, he adds. 

These chemicals can also impact how well our bodies respond to antibiotics and, in certain cases, can trigger antibiotic resistance.

“This is significant because we are at a higher risk of developing infections as well as more chronic diseases,” Jessica Varghese, PhD, an associate professor of nursing at New York Institute of Technology, says.

One major challenge is that many of the chemicals in our foods are difficult to detect. Forever chemicals—known as per- and polyfluoroalkyl substances (PFAS)—are made up of many different molecules, which are listed under different names, according to Dr. Varghese. “So, you can’t just look at your detergent to see if it has ‘PFAS’ in it,” she says.

Related: Blame these pervasive chemicals for poor sleep

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