Do pesticides affect your gut microbiome?

Herbicides, insecticides, fungicides, rodenticides — if you find these words confusing, you’re not alone. They’re all different types of pesticides that farmers spray on crops to kill insects, fungi, and weeds, which might otherwise destroy the plants.

Pesticides are a key component of the global food production system, and they boost yields to feed our growing population. But some of them are harmful to human health and the environment.

The World Health Organization (WHO) and government agencies like the U.S. Food and Drug Administration (FDA) set limits for the safe use of pesticides.

But experts continue to debate their effects on the human body as more evidence emerges that they have a bigger impact than we previously thought.

In this article, we take a closer look at how pesticides might influence your gut microbiome — the trillions of bacteria and other microbes that live in your gut.

At ZOE, we know that maintaining a diverse gut microbiome is beneficial to your health.

Before we get into specifics, we should note that research is still ongoing. 

Due to the known risks of pesticides for health, researchers have focused mainly on animals, and there are no hard conclusions about their impacts on the gut microbiome.

Let’s first look at pesticides in a bit more detail.

Introducing pesticides

Pesticides are chemicals that farmers apply to crops to protect them against pests, weeds, and disease. They play a major role in food production by boosting yields and the number of times a crop can grow on the same land.

As of 2019, roughly 2 million tonnes of pesticides were used every year worldwide, and researchers estimated that just 1 year later this figure would have risen to 3.5 million tonnes.

Although they prevent crop losses, pesticides are toxic and pollute the environment by building up in soil and water. In 2001, 152 countries signed the Stockholm Convention, a global treaty to ban or restrict the agricultural use of several dangerous chemicals.

To manage the risks associated with pesticides, the United Nations Food and Agriculture Organization (FAO) regularly updates guidelines and standards for their use.

Pesticides in food

As your food journeys from farm to fork, so do pesticides.

Once farmers have harvested their crops, they usually wash fresh produce to remove visible soil and other sources of contamination. However, this procedure often doesn’t get rid of pesticides completely.

In a study looking at apples, researchers found that a homemade solution with baking soda was more effective in removing pesticide residues than the standard 2-minute commercial washing method with Clorox bleach. 

The baking soda mixture was also more effective than rinsing apples under tap water. Even using the mixture, it took the scientists 12 to 15 minutes to completely wash off pesticide residues.

What’s more, pesticides don’t stay on the surface of crops — some chemicals leach into the produce. In the same study, the researchers found that 20% of the antifungal pesticide thiabendazole had penetrated the apple skin, and they could only remove the chemical by peeling.

We’ll talk about the best ways to limit your intake of pesticides in a bit.

Pesticide residues

Studies have shown that pesticides can have adverse effects on human health in unsafe amounts, including potentially putting people at greater risk of type 2 diabetes and breast cancer.

That’s why experts conduct regular risk assessments and establish international maximum residue levels for pesticides in food.

But a report by the Environmental Working Group (EWG) published this year suggests that 70% of non-organic fresh produce sold in the U.S. contains residues of potentially harmful pesticides.

This report is based on nearly 45,000 food samples collected by the U.S. Department for Agriculture (USDA) and the FDA. It gives consumers information about pesticide residues.

Before testing for pesticides, the USDA washes and peels produce to mimic how consumers handle food at home. This helps to reflect their daily exposure.

In 2022, the highest levels of pesticide were found in: 

  • strawberries

  • spinach

  • kale, collard, and mustard greens

  • nectarines

  • apples

  • grapes

  • peppers

A single sample of kale, for example, contained traces of up to 21 different pesticides.

On the flip side, the EWG’s “Clean Fifteen” includes:

  • avocados

  • sweetcorn

  • pineapple

  • onions

  • papaya

  • sweet peas (frozen)

  • asparagus

Less than 2% of samples of these fruits and vegetables had detectable amounts of pesticide.

Troublingly, the USDA doesn’t analyze pesticide residues on cereals and grains. Tests commissioned separately by the EWG revealed that oat-based products often exceed residue limits considered protective of health.

As Prof. Tim Spector — ZOE’s scientific co-founder and gut microbiome expert — explains in his new book Food for Life

“While nearly every grain grown today gets some exposure to pesticides and herbicides, oats, which are often grown in damp conditions, get extra treatment and they also retain and absorb the chemicals more than other plants. The ten most common breakfast foods in the U.S. all contain detectable glyphosate levels, but oatmeal has by far the highest levels.”

Although regulations should ensure that levels of pesticides in food are safe, experts think they might have a subtle influence on your metabolic health.

Bad news for the gut microbiome?

Your gut microbiome is in direct contact with the foods you eat and, therefore, with pesticide residues.

At ZOE, we know that having many different beneficial bugs in your gut promotes health. But not all bugs are equal, and certain “baddies” have been linked to negative health outcomes.

Much of the research into pesticides and gut bacteria is in animals. While scientists are still gathering evidence, a review of 117 studies suggested that eating pesticides can disrupt your gut microbiome.

Let’s look at two examples of pesticides and how they might impact your gut.


Glyphosate is the most widely used pesticide in the U.S. and worldwide. It kills weeds by blocking an essential protein-making step in some plants and microbes.

The general view is that glyphosate is harmless for humans because we don’t have this metabolic pathway — but it turns out some of our gut microbes do.

In a 2-year-long study, scientists fed rats Roundup, a herbicide that contains glyphosate. 

The authors found a direct effect on the gut microbiome, including a decrease in Firmicutes bugs, two of which our PREDICT study — the largest study of human nutrition and health of its kind in the world — has identified as “good” gut microbes.

Interestingly, the researchers recorded these effects in female rats but not males, which might be due to different hormones that interact with the microbiome.

Researchers found similar results in a study on rats comparing the effects of glyphosate and Roundup exposure for 35 days on the gut microbiome. Both chemicals were associated with a decrease in Firmicutes bugs.

The authors recorded significant changes in pups but not adults, suggesting that glyphosate could be particularly harmful in the early development of the microbiome.

Another study linked glyphosate to inflammation in the small intestine of rats and to significant disruptions to the gut community, including a decrease in Firmicutes bugs.

Similar to rats, Firmicutes is a dominant family of “good” bugs in humans. They help maintain your gut lining, protecting you from disorders like irritable bowel disease and type 2 diabetes.

While results in rodents don’t necessarily match what happens in humans, the evidence suggests that glyphosate can disturb the gut microbiome.

ZOE’s Senior Nutrition Scientist Dr. Emily Leeming says:

“The pesticide glyphosate is non-toxic to humans, but there might be secondary effects on health. Some evidence in bees and rats found that glyphosate was linked to increased pathogens and reduced beneficial gut bacteria like Lactobacillus and butyrate-producing bacteria.”


Chlorpyrifos is a powerful and broad-spectrum insecticide. The U.S. Environmental Protection Agency banned its use on food crops this year due to potentially toxic effects on the brain.

The European Union and Canada have also banned chlorpyrifos, but it remains widely used across the world and often exceeds limits in food products.

In a study on mice, scientists linked chlorpyrifos to weight gain and higher blood sugar levels. The chemical weakened the gut lining and triggered shifts in microbes, leading to an inflammatory state associated with obesity and metabolic syndrome.

Using a model of the human gut, another study found negative changes in microbiome composition and diversity after 30 days of exposure to low doses of chlorpyrifos.

Specifically, the researchers recorded higher numbers of “bad” bacteria like E. coli — a bug we have nicknamed Esther at ZOE that is associated with a less favorable fat profile. They also found a decrease in beneficial bifidobacteria like our Billy.

A two-way street

We don’t know for sure whether pesticides influence our gut bacteria, but it’s looking likely. While evidence from animal studies is piling up, exploring these effects in humans remains a challenge.

What we do know is that the gut microbiome plays a protective role against some toxins.

Your gut bacteria interact with pesticides and other environmental pollutants. Studies have shown that your microbiome can metabolize some chemicals and make them less toxic.

However, as we’ve seen above, pesticides may disrupt your gut community and harm the “good” bugs that keep you healthy while promoting some “bad” bugs.

These changes could actually prevent your microbiome from dealing with chemicals properly and lead to negative health outcomes in the long term.

How to lower your pesticide exposure

The picture will grow clearer as scientists continue to gather evidence. We should also note that experts regularly review the science to keep standards for pesticides up to date.

In the meantime, there are ways you can limit your intake of pesticides in food.

For example, you might want to consider eating organic food if possible. Organic food is grown without synthetic pesticides.

Although there are no definite conclusions about organic diets, research suggests some health benefits of increased organic intake, like lower body weight and reduced incidence of allergies and metabolic syndrome.

If organic food is inaccessible to you, make sure to wash fruit and veg thoroughly under running water or soak them in warm water with vinegar or baking soda. You can also scrub firm produce like potatoes or peel the skin off to get rid of residues.

If you eat meat or fish, you might want to trim the fat and skin to reduce your intake of pesticides that accumulate in fatty tissue.

What’s the deal, in a nutshell?

Scientists have established that exposure to some pesticides in food has a negative impact on health. Now, researchers are turning toward their potential effects on our gut bacteria.

So far, studies in rodents have suggested that widely used pesticides like glyphosate and chlorpyrifos lead to shifts in the composition and function of the gut microbiome.

These disruptions have been linked to metabolic disorders and may be a factor in the current epidemic of inflammation-related diseases like obesity and diabetes.

At ZOE, we know that a diet with plenty of fruit, vegetables, and whole foods is important to maintain a healthy gut. 

Although you might want to limit your pesticide intake, the benefits of eating a variety of fresh foods like dark green vegetables strongly outweigh the potential risks of pesticide residues.


A systematic review of organic versus conventional food consumption: Is there a measurable benefit on human health? Nutrients. (2020).

Changes in composition and function of human intestinal microbiota exposed to chlorpyrifos in oil as assessed by the SHIME model. International Journal of Environmental Research and Public Health. (2016).

Effectiveness of commercial and homemade washing agents in removing pesticide residues on and in apples. Journal of Agricultural and Food Chemistry. (2017).

EPA takes next step to keep chlorpyrifos out of food, protecting farmworkers and children’s health. (2022).

EWG’s 2022 Shopper’s Guide to Pesticides in Produce. (2022).

Glyphosate exposure induces inflammatory responses in the small intestine and alters gut microbial composition in rats. Environmental Pollution. (2020).

Gut microbiota: an underestimated and unintended recipient for pesticide-induced toxicity. Chemosphere. (2019).

Human health risk assessment on the consumption of fruits and vegetables containing residual pesticides: a cancer and non-cancer risk/benefit perspective. Environment International. (2017).

New round of EWG testing finds glyphosate in kids’ breakfast foods from Quaker Oats, General Mills. (2018).

Organophosphorus pesticide chlorpyrifos intake promotes obesity and insulin resistance through impacting gut and gut microbiota. Microbiome. (2019).

Prospective association between dietary pesticide exposure profiles and postmenopausal breast-cancer risk in the NutriNet-Santé cohort. International Journal of Epidemiology. (2021).

Prospective association between dietary pesticide exposure profiles and type 2 diabetes risk in the NutriNet-Santé cohort. Environmental Health. (2022).

Sex-dependent impact of Roundup on the rat gut microbiome. Toxicology Reports. (2017).

Stockholm Convention. (n. d.).

The gut microbiota: a major player in the toxicity of environmental pollutants? Nature Partner Journals Biofilms and Microbiomes. (2016).

The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiome. Environmental Health. (2018).

Toxicology and microbiota: How do pesticides influence gut microbiota? A review. International Journal of Environmental Research and Public Health. (2021).

Worldwide pesticide usage and its impact on ecosystem. SN Applied Sciences. (2019).