11
Jun
Study Maps the Gut Microbiome and Adverse Impacts of Pesticide Residues
(Beyond Pesticides, June 11, 2025) Researchers developed a novel tool* in a recent study published in Nature Communications this year that successfully creates a map of the “pesticide-gut microbiota-metabolite network,” identifying “significant alterations in gut bacteria metabolism.”
While the study authors acknowledge that this is not a complete map, since they selected specific pesticides and bacterial partners, the research adds to the body of peer-reviewed scientific literature that underscores the relationship between pesticide residues and human gut health. Organic farmers, as well as any land steward invested in agroecological practices and soil health, understand that microbial life (both in the body and in the soil) is dangerously undermined by the status quo of chemical-intensive land management.
Background and Methodology
The researchers leverage mass spectrometry to test metabolite (metabolomics) and lipid (lipidomics) relationships with pesticide residues, as well as an in vivo mouse model. *The map itself is a form of computational biology, which advocates have warned could be a false solution if not accompanied by other proven scientific methods. See here for analysis by the Natural Resources Defense Council on risks of unproven methods such as New Approach Methodologies [NAMs].
All major phylogenetic (“evolutionary relationships among biological entities”) groups are represented in the bacterial strains studied: 7 Bacteroidetes, 7 Firmicutes, 2 Actinobacteria, and 1 Proteobacteria. There were 18 pesticide compounds (active ingredients and metabolites) tested in relation to the above bacterial strains, including organochlorines (endosulfan, methoxychlor, and DDT metabolites 4,4’-DDT, 4,4’-DDE, 4,4’-DDD); organophosphates (chlorpyrifos, chlorpyrifos metabolite TCP [3,5,6-Trichloro-2-pyridinol], dichlorvos, malathion, fenitrothion, parathion, diazinon); pyrethroids (permethrin and cypermethrin); carbamates (carbaryl), glyphosate, and malathion dicarboxylic acid (metabolite of malathion).
Results
The researchers signal that microbial metabolite and lipid profiles can serve as biomarkers for environmental exposure and disease diagnosis; however, more studies are necessary.
Key findings identified by the researchers who conducted this study include:
- 306 pesticide-bacteria pairs showing significant potential metabolic shifts in the gut microbiome.
- 40 metabolic pathways are disrupted; more specifically, pathways involving nucleotide synthesis, amino acid metabolism, and tryptophan, propanoate, and bile acid pathways. This is critical to understanding of public health, as nucleotides are considered one of the building blocks of RNA and DNA (National Human Genome Research Institute), amino acids are important energy sources for the human body (Nature), tryptophan and propanoate serve essential functions for metabolic regulation (Endocrinology) and bile acid is critical for disposal of toxic metabolites and absorption of lipid-soluble vitamins and essential dietary fats. (ScienceDirect).
This in vivo mouse study also validated these metabolic changes based on the bacterial-pesticide relationship. For example, mice in this study that were recolonized with B. ovatus and exposed to 4,4′-DDE exhibited:
- Systemic metabolic changes identified in the brain, liver, intestine, and lung, among other organs.
- Altered levels of lipids, purines (building block of DNA and RNA), N-acylethanolamine (NAEs), short-chain fatty acids (SCFAs), and bile acids (BAs).
- Suppression of TLR4/NF-κB inflammatory signaling, indicating microbial modulation of host immunity.
- Measurable pesticide residues in tissues, including the brain and gut.
Previous Research
There has been mounting scientific evidence in recent years that identifies various exposure pathways of concern that may be contributing to poorer health outcomes for the gut microbiome, as documented in previous Daily News reports, and the Pesticide-Induced Disease Database.
University of Illinois researchers in 2020 published a literature review in Toxicological Sciences looking at how various environmental contaminants adversely affect and reinforce chemical disruption of the gut microbiome. The review details manufacturing compounds in commonly-purchased consumer products, like bisphenols (BPA) and phthalates in plastic packaging and vinyl flooring. The review also examines the science behind the exposure to numerous persistent organic pollutants (POPs) like pesticides, polychlorinated biphenyl (PCBs), perfluorochemicals (PFCs) in non-stick cookware, polybrominated diphenyl ethers (flame retardants), and dioxins (byproducts of pesticide manufacturing and burning organic material like fossil fuels). The research highlighted in this review looks at the adverse impacts of these chemicals in rodents (e.g., rats, mice), aquatic organisms (e.g., fish, amphibians), birds (e.g., chickens), larger mammals (e.g., dogs, cows, human adults, and infants), insects (e.g., honey bees), and other organisms. (See Daily News here.)
In 2022, a robust report published in Environmental Health and developed in partnership with researchers at King’s College London, the Center for Microbiome Analyses and Therapeutics (Netherlands), the Metabolomic Medicine Clinic (Greece), and the University Hospital of Limoges (France) identified over 300 environmental contaminants in collected fecal and urine samples. The report examined dietary exposure to 186 common pesticide residues in the fecal excrement to determine impacts on the microbiome among 65 twins in the United Kingdom and investigated if associations between gut health and various variables can also impact concentrations of pesticide residues in excrement to indicate gut health alterations. In terms of pesticide residues, the report finds that all urine samples contain pyrethroid or organophosphate insecticide residues, with 53 percent of urine samples containing glyphosate. Additionally, participants who consume more fruits and vegetables grown with chemical-intensive practices have higher concentrations of organophosphate residues. Although urinary metabolite (pesticide breakdown product) excretion lacks a correlation with gut microbial changes, there are 34 associations between the concentration of pesticide residues and metabolite residues in fecal matter and gut health. Glyphosate excretion in the fecal matter correlates with an increase in bacterial species richness, fatty acid metabolites, and phosphate concentrations in the gut. For pyrethroids, the deltamethrin metabolite, Br2CA, has a positive association with phytoestrogens enterodiol (dietary estrogen) and a negative association with specific amino acids in the gut. (See Daily News here.)
Specific pesticides and classes of pesticide active ingredients, such as glyphosate, neonicotinoids, azoxystrobin, among others, have been linked to adverse human gut health impacts. Researchers based at the University of Turku (Finland) developed a bioinformatics tool in 2021 to determine that “54% of species in the core human gut microbiome are sensitive to glyphosate.” (See Daily News here.) Researchers published a study in the World Journal of Pediatrics, finding an association between antibiotic and neonicotinoid (neonic) exposure and the onset of pediatric (childhood) type 1 diabetes (T1D) through its effects on the gut microbiome. This can have a compounding effect on afflicted participants, as children with type 1 diabetes are at higher risk of other autoimmune disorders, including thyroid and celiac disease. (See Daily News here.) The widely used fungicide azoxystrobin has been linked to disrupting the function of the intestinal (colonic) barrier responsible for the absorption of nutrients and defense against harmful substances. This function is critical to the health of the gut microbiome. This study demonstrates that exposure alters the ability of gut bacteria to break down proteins, fats, carbohydrates, or other macronutrients into residual metabolites, which constitute the metabolic profile. (See Daily News here.)
For more information on the importance of soil health and “the underground ecosystem” to the gut microbiome, please see our “Letter from Washington” and the work of David Montgomery, PhD, featured speaker at Beyond Pesticides’ 35th National Pesticide Forum.
Call to Action
Public health and environmental advocates are calling for solutions grounded in science. It is critical that agencies charged with protecting the food supply chain move forward in such a manner, including the U.S. Department of Health and Human Services (HHS) and the U.S. Department of Agriculture (USDA). See here to contact HHS Secretary Robert F. Kennedy, Jr, to revise the memorandum of understanding (MOU) with the U.S. Environmental Protection Agency (EPA) on pesticide residues and set more protective standards.
All unattributed positions and opinions in this piece are those of Beyond Pesticides
Source: Nature Communications
