Microbiota Changes

also see digestive tract, soils, Organophosphates, cancer/ links 2, health/low dose effects , Soils- Pesticides in

Widespread pesticide use harms soils life (PAN Europe - pane -  February 23, 2026) 

• The presence of pesticides were found to be, after soil properties, the second widest driver of soil biodiversity patterns
• At 70% of the sites, one or more pesticide residues were found. In total, 63 different pesticides were detected
• The majority of pesticides detected were fungicides (54%), followed by herbicides (34.9%) and insecticides (11.1%)
• While highest numbers of residues were, as expected, found in croplands, pesticides were also present in the other sites. Associations between pesticides and soil biodiversity were consistent among analyses for croplands and other sites. 
• Pesticides alter microbial functions, including nitrogen and phosphorus cycling
• Pesticides negatively impact beneficial soil taxa, 
• Increasing concentrations of certain fungicides were found to reduce richness and diversity of archaea, bacteria, protists, nematodes and arthropods. 
• soil organisms harmful to plant growth, e.g. fungal plant pathogens, herbivore nematodes and protist plant parasites, were positively affected by increased concentration of certain pesticides, such as the herbicides pendimethalin and glyphosate.

Variability in Effect of Pesticides on Bumblebee Survival Tied to Gut Microbiome Health    (Beyond Pesticides, July 18, 2025) A study in Royal Society Open Science shows intraspecific differences (between individuals of a species) in wild bumblebees (Bombus vosnesenskii) exposed to an herbicide (glyphosate), a fungicide (tebuconazole), and an insecticide (imidacloprid), with gut microbiome health as a factor. 

dding to Wide Body of Science, Study Finds Pesticide Residues Threaten Health of Soil Microbiome   (Beyond Pesticides, May 13, 2025) 'A study in Environmental Pollution examines ecological and health risks in farmland soil with pesticide contamination. ...the study finds that “more than ten pesticides were detected in 98.62% of the soil samples, which changed the soil environment” and threatens the health of the soil microbiome. ... (the authors) assess 50 selected pesticides in 145 soil samples from agricultural land in Zhejiang Province, China and calculate the associated risks to ecosystems and public health.     145 soil samples were obtained from citrus orchards (26), vineyards (29), and vegetable gardens (90) and range in crop types,. Each sample was analyzed for pesticide residues and physicochemical properties such as total nitrogen, pH, and organic matter.      From the health risk assessment, the calculations identify high carcinogenic risks from dimethomorph, imidophos, indoxacarb, and imidacloprid.       Within the ecological risk assessment, nightshade vegetables were the planting type with the highest average, and the insecticides chlorpyrifos and bifenthrin were identified as having higher entropy (uncertainty) values, classifying them as ‘medium ecological risk threats.’      “The vineyard soil had the most unique species (1,059) among all planting types. As the type with the most serious pesticide residue pollution and highest ecological risk, nightshade land had only 52 exclusive species.”      The soil microbial communities were most impacted by dimorpholine, and the “soil bacterial composition changed significantly under different ecological risk levels at the phylum level .” Of the bacteria, Firmicutes exhibit the clearest response to pesticide residues. .. Altering the abundance of Firmicutes, and any soil biota, leads to impacts on soil health and crop productivity.  .. these bacteria may be an indicator of the ecological risk of pesticides.'    SNAP Comment: As of June 2025, there are 4 (down from 7) dimethomorph, 0 imidophos, 0 indoxacarb, 94 (down from 138) imidacloprid, 0 (down from 297) chlorpyrifos and 0 (down from 4) bifenthrin were containing pesticides registered for use in Canada. 

Ecosystem consequences of herbicides: the role of microbiome (opinion)
 (Suvi Ruuskanen et al, Trends in Ecology & Evolution, Volume 38, Issue 1, January 2023, Pages 35-43)      'While many herbicides were initially considered safe for non-target taxa as their mechanism of action was thought to be absent in these organisms, it has been understood only recently that herbicides may have profound effects on non-target taxa via alterations of microbial communities and microbial function in soil, plants, and animals 3,4 (Table 1). Given the imperative role of microbes in driving ecoevolutionary adaptations since the origin of life, and that microbes and their hosts comprise coevolving, multipartite entities, holobionts 5, a comprehensive understanding of the risks associated with altered microbiomes is needed 6. Here, we propose that herbicides can influence natural and agricultural ecosystem functioning due to soil- and host-associated microbiome alteration (Figure 1) and may have evolutionary consequences. ' 

More Data Finds Long-Term Exposure to Toxic Pesticides Alters Human Gut Microbiome and Metabolism   (Beyond Pesticides, April 26, 2024) Researchers build on existing research when assessing the relationship between long-term exposure to organophosphorus pesticides—widely used in food production and homes and gardens—and the human gut microbiome. In a new study published in Environmental Health, an interdisciplinary research team from University of California, Los Angeles determined, “that exposure to organophosphorus pesticides is associated with changes in the abundance of several bacterial groups and differential functional capacity in metabolic pathways supported by the human gut microbiome.”

Weed Killer Use Destroys Soil Life and Ecosystems, Paper Finds   (Beyond Pesticides, November 11, 2022) 'A paper published in Trends in Ecology & Evolution in late October sounds an unnerving alarm about the globally ubiquitous use of herbicides and the ecological destruction being caused. It asserts that widespread environmental contamination with these herbicide compounds is influencing soil, plant, and animal microbiomes in ways that are not only not well understood, but also, can have significant impacts on the functioning of organisms and their ecosystems — with evolutionary implications. '   'The study authors also note that adjuvant, “inert” ingredients in herbicide formulations can sometimes be even more toxic to non-target organisms than the active ingredients themselves,' In the US, these are untested for that effect and also secret. They are also secret in Canada but I am unsure if they have been tested for effects on non-target organisms. Likely not.   'The study identifies classes or modes of action for a host of herbicide active ingredients, including whether they act directly or indirectly on microbiota, and their respective effects on soil, plant, or animal microbiomes. Among the modes (and sample compounds) that have direct impacts on microbes are:

• ACC (acetyl-CoA carboxylase) inhibitors (e.g., diclofop-methyl, haloxyfop)
• ALS (acetolactate synthase) inhibitors (sulfonylureas, triazolopyrimidines)
• EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) inhibitors in the shikimate pathway (glyphosate)
• glutamine synthetase inhibitors (glufosinate)The mechanisms that exhibit indirect impacts, including on cellular metabolism and hormone synthesis, are auxin-like herbicides (2,4-D, dicamba); photosystem (related to photosynthesis) inhibitors (triazines, paraquat, diphenyl ether); and gibberellin (plant hormone that stimulates stem elongation, germination, and flowering) inhibitors (acetochlor, metolachlor, pendimethalin).
• The indirect impacts on microbiota include those that degrade bacterial diversity, erode microbial community structure, and disable nitrogen-fixing bacteria.'

Glyphosate study shows adverse health effects at "safe" dose  (GM Watch, 16 May 2018) 'The study was focused on the newborn, infancy and adolescence phases of life. The results reveal that glyphosate-based herbicide (GBH) was able to alter certain important biological parameters, mainly relating to sexual development, genotoxicity, and the intestinal microbiome....The effects occurred at a dose deemed safe by regulators to ingest on a daily basis over a long-term period. In human-equivalent terms the dosing period corresponded to the period from the embryo stage to 18 years of age.' The levels measured in urine suggest 'a bioaccumulation effect of glyphosate that was proportional to the length of treatment.'      more on glyphosate at fact sheets/ glyphosate

Study finds link between pesticide exposure and microbiome changes (UPI, By Brooks Hays. Nov. 11, 2016)  The oral microbiome of farmworkers are markedly different than other humans, and pesticide exposure explains why, new research shows. Adults with concentrations of organophosphate pesticide, Azinphos-methyl, in their blood had a significantly altered oral microbiome. "We found significantly reduced abundances of seven common taxa of oral bacteria, including Streptococcus, one of the most common normal microbiota in the mouth," researcher Ian B. Stanaway said in a news release. Researchers also found a correlation between pesticide exposure and shifts in the abundance and diversity of several other strains and species of bacteria, including microbes belonging to genera Streptococcus and Halomonas. Additionally, scientists measured shifts in bacterial diversity related to changing levels of exposure during the seasons. "The challenge becomes, what does this mean," said researcher Elaine M. Faustman. "We don’t know, but we depend on the micriobiome for many metabolic processes." link to study. SNAP Comment: This is the first study I know of that has looked at this issue. Although it specifically studies the organophosphate Azinphos-methyl, I would not be surprised that the link also exists with other pesticides. Time will tell. According to PMRA label search (15 Nov 2016), Azinphos-methyl is no longer sold in Canada. I did not check every historical label but the last sale I could find was in 2010. It could still be used by those with a stockpile.