Pesticides and the gut microbiome

The microbiome refers to the dense and diverse microbial community that lives in the intestines of mammals, including humans. Gut microbiota and their metabolites play a crucial role in determining and safeguarding health. The microbiome not only helps digest food and extract nutrients, it shapes and protects the immune system, produces vitamins, guards against pathogens, contributes to metabolic and neurological health and influences disease risk and treatment response.

The growing realisation of the importance that the microbiome holds for our very existence, has even started to shift perceptions of the human body. Many scientists consider the body a superorganism, characterised by a partnership between human and microbial cells working together. Extraordinarily, it’s estimated that the total number of microbial cells in a typical human — around 39 trillion, is greater than the number of actual human cells, which is around 30 trillion (1).

‘Pesticide’ is an umbrella term for substances designed to eliminate weeds, pests or disease, and includes insecticides, herbicides and fungicides. Because pesticides are widely used in agriculture and in public spaces such as parks, they are now ubiquitous in both the environment and our diets. There is a substantial and growing body of research linking pesticide exposure to a range of human health issues including endocrine, neurological and reproductive problems (2).

Attempts are made to limit the impact of our exposure to pesticides. The Maximum Residue Limit (MRL) is the highest level of pesticide residue that is legally tolerated when pesticides are applied correctly on the farm. The Acceptable Daily Intake (ADI) represents the amount of a substance that a person can consume daily over a lifetime without risk to health.

Yet this regulatory approach has a number of flaws, two of which we’ll focus on now.

Safety regulations around pesticides are made on a pesticide-by-pesticide basis, they don’t take into account the impact of being exposed to multiple pesticides at once, or how those pesticides might interact with one another. Yet there’s evidence that these so-called pesticide ‘cocktails’ are a problem.

A report co-authored by the Soil Association and Pesticide Action Network (PAN) UK (3), highlighted research showing that combined actions of pesticide mixtures can lead to the creation of cancer cells and disruptions to the endocrine system. Alarmingly, even when doses of individual chemicals are below regulatory safety levels, pesticide mixtures have been associated with obesity and impaired liver function (4). It’s not just human health at risk from pesticide cocktails. Studies looking at insects, fish and birds show similar results. One study found that when a commonly used fungicide is combined with a certain insecticide claimed to be a ‘safe’ replacement for neonicotinoids, the result was more toxic to bees than when the chemicals appeared alone (5).

The Dirty Dozen

Pesticide cocktails are a common reality in food on UK shelves. Each year, the UK government publishes data on pesticide residues in food consumed in the UK. PAN UK analyse the results and publishes the Dirty Dozen list of the fruit and vegetables most likely to be contaminated with multiple pesticides (6). The latest data from the 2024 government testing programme revealed that two or more types of pesticide residues were found on 99% of grapefruit, 90% of grapes, 79% of limes and 67% of the nation’s favourite fruit — the banana (6).

The other fruit and vegetables in the top 12 list were peppers, melons, beans, chillis, mushrooms, broccoli, aubergines and dried beans. The selection of fruit and vegetables sampled by the government changes slightly every year so it’s not always possible to make year-on-year comparisons. But data over the last five years always finds citrus fruits near the top of the list. Of all the fruit and vegetables tested in 2024, 123 different pesticide active substances were detected, 12 PFAS aka forever chemicals, 42 carcinogens and 36 pesticide active substances that are not actually approved for use in the UK. 

Alongside fruit and vegetables, the government also tested bread samples and wheat flour. They found 12 different pesticide active substances including four Highly Hazardous Pesticides (HHPs). Of bread samples, 47% contained multiple pesticide residues. Glyphosate was found in 28% of the bread tested. This is likely related to the chemical’s use as a pre-harvest desiccant — a practice now banned in the EU but still permitted in the UK. This is just one example of where the UK is lagging behind the EU when it comes to pesticide regulation.

Another area where regulation isn’t keeping pace with scientific understanding is in relation to the gut microbiome. For example, British scientists at Cambridge University are producing some of the most important research in the world on how pesticides harm gut bacteria (7), yet UK regulators are assessing food safety using frameworks that don’t account for microbiome effects at all.

The situation with the world’s most widely-used herbicide — glyphosate, is a good case in point. Glyphosate works as a powerful herbicide by inhibiting what’s known as the shikimate pathway. This biochemical pathway is present in plants but not humans, which is the key reason why it is claimed by its proponents to be safe. However, the shikimate pathway is present in bacteria and fungi in the gut microbiome.

In 2025, a comprehensive carcinogenicity study (8) conducted by scientists from Europe and the US found that even at doses considered safe, glyphosate caused multiple types of cancer in rats. The study is the latest in a line of alarming scientific findings related to glyphosate. The International Agency for Research on Cancer (IARC) label it as a probable carcinogen, but regulators are yet to take more drastic action.

Glyphosate isn’t the only pesticide raising a cause for concern in relation to the gut microbiome. A recent study published in Nature Communications (9) created a map of the “pesticide-gut microbiota-metabolite network”. It identified significant alterations in gut bacteria metabolism across 306 pesticide-bacteria pairs, with 40 metabolic pathways disrupted. These included ones involved in nucleotide synthesis (the building blocks of RNA and DNA), amino acid metabolism (energy sources for the body), tryptophan and propanoate (important in metabolic regulation), and bile acid pathways (critical for disposing of toxic metabolites and mineral absorption).

A growing body of research suggests that the gut plays an important role in the development of Parkinson’s disease too. Evidence points to organophosphate pesticides as a possible trigger for gut barrier damage that may lead to neurological changes decades before any symptoms appear (10).

In 2023 the United Nations’ Food and Agriculture Organisation (FAO) published a literature review (11) looking at the impact of pesticide residues on the gut microbiome and human health. It noted significant research gaps, particularly on chronic exposure to low-level pesticide residues and the microbiome’s role in the chemical transformation of pesticides (which can alter their toxicity).

It also called for better definitions of a healthy microbiome and the different types of disruption that can take place, plus better standardisation of methodologies to make testing and study results comparable, thus potentially more translatable into regulatory action. It is certainly a concern that the UN’s own food safety body is indicating that current pesticide safety assessments are incomplete because they don’t account for gut microbiome effects.

As the body of evidence on the problematic interactions between pesticides and the gut microbiome continues to grow, it’s important that we act where we can. On a personal level, choosing organic produce can limit dietary exposure to pesticides. On a broader level, contacting MPs and regulators to raise your concerns about the issues and add to the public pressure. Also, you can share information and support organisations like the Soil Association and Pesticide Action Network (UK) who are working directly to drive change at a practical and political level on this important topic.

1. BBC Science Focus Magazine. The human microbiome: everything you need to know about the 39 trillion microbes that call our bodies home. BBC Science Focus Magazine. https://www.sciencefocus.com/the-human-body/human-microbiome. Accessed March 2026.
2. Filipoiu DC, Bungau SG, Endres L, et al. Global evidence on monitoring human pesticide exposure. J Xenobiot. 2025;15(6):187. https://doi.org/10.3390/jox15060187
3. Pesticide Action Network UK; Soil Association. The Cocktail Effect. Pesticide Action Network UK. https://www.pan-uk.org/the-cocktail-effect. Accessed March 2026.
4. Docea AO, Gofiță E, Goumenou M, et al. Six months exposure to a real life mixture of 13 chemicals’ below individual NOAELs induced non monotonic sex-dependent biochemical and redox status changes in rats. Food Chem Toxicol. 2018;115:470–481. https://doi.org/10.1016/j.fct.2018.03.052
5. Tosi S, Nieh JC. Lethal and sublethal synergistic effects of a new systemic pesticide, flupyradifurone (Sivanto®), on honeybees. Proc Biol Sci. 2019;286(1900):20190433. https://doi.org/10.1098/rspb.2019.0433
6. Pesticide Action Network UK. Dirty Dozen 2025. Pesticide Action Network UK; 2025. https://www.pan-uk.org/site/wp-content/uploads/Dirty-Dozen-2025.pdf. Accessed March 2026.
7. Roux I, Lindell AE, Grießhammer A, et al. Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro. Nat Microbiol. 2025;10(12):3107–3121. https://doi.org/10.1038/s41564-025-02182-6
8. Panzacchi S, Tibaldi E, De Angelis L, et al. Carcinogenic effects of long-term exposure from prenatal life to glyphosate and glyphosate-based herbicides in Sprague–Dawley rats. Environ Health. 2025;24:36. https://doi.org/10.1186/s12940-025-01187-2
9. Chen L, Yan H, Di S, et al. Mapping pesticide-induced metabolic alterations in human gut bacteria. Nat Commun. 2025;16:4355. https://doi.org/10.1038/s41467-025-59747-6
10. Zhang K, Paul K, Jacobs JP, et al. Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study. Environ Health. 2024;23(1):41. https://doi.org/10.1186/s12940-024-01078-y
11. Food and Agriculture Organization of the United Nations. Pesticide Residues in Food and the Human Gut Microbiome: A Literature Review. FAO; 2023. https://openknowledge.fao.org/server/api/core/bitstreams/d1389309-c6fc-4412-882a-425f1143ecfd/content. Accessed March 2026.