A new scientific review raises questions about glyphosate’s effects on the bacteria living inside us — and whether regulatory safety assessments are keeping pace with the evidence.
If the science increasingly recognises that glyphosate can affect organisms living inside mammals, should regulatory assessments continue to rely on the absence of glyphosate’s target pathway in mammalian cells as reassurance?
For decades, one of the central arguments supporting glyphosate’s safety has been relatively straightforward. The herbicide works by disrupting a biochemical process found in plants but absent from human and other mammalian cells. Without that process, the reasoning goes, glyphosate has no equivalent target in our bodies.
But there is something missing from that explanation.
Our bodies are home to trillions of microorganisms, including bacteria that perform essential functions in digestion, metabolism, immune regulation and maintaining the intestinal barrier. Many of these organisms possess the very biochemical pathway that glyphosate was designed to inhibit.
So what happens when a chemical that targets this pathway encounters the microorganisms living inside us?
A new scientific review published on 6 October 2026 in the Journal of Applied Toxicology examines precisely that question. Led by researcher Robin Mesnage, the paper critically evaluates evidence from experimental and observational studies investigating how glyphosate and glyphosate-based herbicides affect the mammalian gut microbiome.
The review brings together a growing body of experimental evidence showing that glyphosate and glyphosate-based herbicides can alter the mammalian gut microbiome, sometimes alongside changes in intestinal function, inflammation and microbial metabolism. These findings challenge a longstanding assumption underlying glyphosate’s safety narrative: that because mammalian cells lack the biochemical pathway targeted by glyphosate, its effects on mammals are necessarily limited. The microorganisms living inside mammals tell a more complicated story.
For New Zealand, where glyphosate remains widely used and has never undergone a comprehensive modern reassessment by the Environmental Protection Authority (EPA), those questions deserve attention.
The Biological Pathway We Don’t Have — But Our Bacteria Do
Glyphosate works primarily by inhibiting an enzyme known as 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), part of the shikimate pathway. Plants use this pathway to produce three essential aromatic amino acids: phenylalanine, tyrosine and tryptophan.
Humans and other mammals do not possess this pathway. We obtain these amino acids through our diets, which is one reason glyphosate has historically been regarded as having relatively low direct toxicity to mammals through this particular mechanism.
However, many microorganisms do possess the pathway, including bacteria that inhabit the digestive tract.
This distinction matters because the gut microbiome is not simply a collection of organisms passing through our intestines. It is a complex biological community involved in processes that influence our health, from breaking down dietary components to producing metabolites and supporting immune function.
Changes in the gut microbiome can have consequences beyond the digestive system, particularly when they involve microbial metabolism, inflammation or the integrity of the intestinal barrier. Understanding whether glyphosate contributes to such changes, and under what exposure conditions, is therefore an important question for toxicological research.
The new review examines whether glyphosate can produce such changes and, importantly, whether the effects observed in laboratory experiments are biologically meaningful.
What the Animal Studies Are Finding
The review identifies controlled rodent studies as providing the most consistent evidence that glyphosate and glyphosate-based herbicides can alter the gut microbiome. Importantly, some experiments have reported effects extending beyond changes in the types and numbers of bacteria present.
Several studies identified alterations in intestinal bacterial communities, including reductions in lactobacilli, a group that includes species associated with normal intestinal function. Researchers also reported changes in microbial metabolism, intestinal inflammation and increased intestinal permeability.
The latter finding is particularly significant. The intestinal barrier performs an essential protective function, helping regulate which substances can pass from the digestive tract into the body’s internal environment. Increased permeability may allow substances to cross that barrier more readily, potentially contributing to inflammatory responses.
But bacteria are not the only microorganisms affected. The review also examines evidence involving the gut mycobiome — the community of fungi living within the digestive tract.
In one rat study, two commercial Roundup formulations altered both bacterial and fungal populations, while glyphosate alone affected the bacterial community but not the fungal community. The formulated products were associated with reductions in commensal fungi and increases in opportunistic fungi.
This matters because the gut microbiome functions as an interconnected ecosystem. Changes in one group of microorganisms may influence others, potentially affecting the community’s ability to prevent opportunistic organisms from becoming established.
The review also examines experiments reporting neurobehavioural, metabolic and reproductive effects alongside changes in the gut microbiome. While the occurrence of these effects together does not necessarily establish causation, some researchers have gone a step further.
In a 2024 study, scientists transferred gut microorganisms from rats exposed to a Roundup formulation into other animals. The recipients subsequently developed aspects of the intestinal dysfunction observed in the exposed animals, including oxidative stress and inflammation. Transplantation of microbiota from healthy animals helped reduce the injury.
A separate 2026 mouse study reported that transferring microbiota from glyphosate-exposed animals into previously unexposed mice reproduced social-behaviour deficits. These findings provide more direct experimental evidence that changes in gut microorganisms can contribute to effects elsewhere in the body.
They do not establish that comparable effects occur in humans. But they move the investigation beyond simply observing an association between glyphosate exposure, microbiome changes and other biological outcomes.
Some of these findings occurred at doses corresponding to regulatory acceptable daily intakes (ADIs). In one rat study, exposure beginning during pregnancy was associated with changes in the gut microbiome of offspring, including reduced Lactobacillus populations, at the European Union ADI. Other studies reported microbiome or metabolic changes at comparable reference doses, although some found little or no significant change.
The findings were not uniform. Results varied according to dose, formulation, sex, diet and the developmental stage at which exposure occurred. Importantly, an alteration in microbial populations at an ADI does not automatically establish an adverse health effect. It does, however, warrant investigation into whether conventional toxicity studies are equipped to detect and evaluate such changes.
Taken together, these studies provide evidence that glyphosate and certain commercial formulations can affect the mammalian gut microbiome under experimental conditions, sometimes accompanied by changes in intestinal physiology.
Glyphosate Alone Is Not Necessarily the Same as the Herbicide Being Sprayed
One of the more significant findings concerns the difference between glyphosate as an individual chemical and the commercial herbicide formulations in which it is sold.
Glyphosate-based herbicides contain additional ingredients, commonly called co-formulants, which help the product spread, penetrate plant surfaces or perform other functions.
The review finds that formulated herbicides are frequently more disruptive to the gut microbiome than glyphosate alone.
In one experiment discussed by the authors, rats exposed to pure glyphosate showed relatively little change in their overall gut microbial community, even at doses substantially above the European Union’s acceptable daily intake. A corresponding commercial formulation, however, altered microbial diversity.
This suggests that ingredients other than glyphosate, or interactions between ingredients, may contribute to the biological effects observed.
It also raises a broader regulatory question.
When a pesticide’s safety is assessed primarily through studies of its active ingredient, how adequately does that assessment represent the complete product used by farmers, contractors, councils and householders?
This is not a new concern. Scientific investigations have previously identified differences between the toxicity of glyphosate alone and that of certain formulated products. But the microbiome adds another dimension to the issue.
A formulation that produces little obvious direct toxicity in mammalian cells could still affect the microorganisms that help maintain normal intestinal function. And because commercial formulations differ in their ingredients and concentrations, findings from one product cannot automatically be applied to another.
That makes formulation-specific testing particularly important. If additional ingredients or interactions between them influence microbiome effects, assessments based predominantly on glyphosate alone may not adequately characterise the biological activity of the complete herbicide.
The distinction between glyphosate and its commercial formulations is only one part of the picture. The review also examines what happens when different pesticide active ingredients are encountered together — a separate question from the effects of co-formulants within an individual product.
In a 2026 rat study, researchers examined glyphosate alongside two other herbicides, 2,4-D and dicamba. When the three chemicals were administered together, each at its respective European Union acceptable daily intake, the mixture produced substantially greater inflammatory responses and changes in intestinal barrier markers than glyphosate alone.
The researchers reported changes consistent with increased intestinal permeability, including reduced expression of genes involved in maintaining the intestinal barrier. Under the conditions of this experiment, glyphosate alone did not produce comparable effects at its acceptable daily intake.
This raises a further question for pesticide regulation. If individual chemicals are assessed separately, how adequately do those assessments account for biological effects arising when several chemicals are encountered together?
For New Zealand, where glyphosate-based products are used in agriculture, public spaces and domestic gardens, the distinction is especially relevant. Are the products being approved and used here adequately assessed for effects that may not be apparent from testing the active ingredient alone?
Why Diet May Change the Results
One particularly interesting aspect of the review is its examination of why some experiments identify significant microbiome effects while others find very little.
The explanation may partly lie in what the animals are eating.
Bacteria use the shikimate pathway to manufacture aromatic amino acids. But when sufficient quantities of those amino acids are already available from their surroundings, bacteria may be less dependent on producing them internally.
In laboratory experiments, supplying additional aromatic amino acids has been shown to reduce glyphosate’s inhibitory effects on bacterial growth.
The digestive tract is also a nutrient-rich environment, continuously receiving dietary proteins and other substances that can influence microbial metabolism.
Consequently, simply demonstrating that a bacterium possesses the shikimate pathway does not prove that glyphosate will inhibit its growth under normal intestinal conditions.
This adds another layer of complexity to glyphosate’s potential effects on the gut microbiome. The presence of the shikimate pathway makes certain bacteria potential targets, but their susceptibility may also depend on nutrient availability and the conditions within the intestinal environment.
The biological outcome depends on the environment in which exposure occurs.
It also suggests that dietary composition may be an important variable when interpreting toxicology studies — and that differences in experimental diets could help explain why researchers sometimes obtain conflicting results.
But What About Humans?
The experimental evidence raises an obvious question: if glyphosate and glyphosate-based herbicides can alter the gut microbiome of laboratory animals, could similar effects occur in humans?
The answer remains uncertain, but the limitations of the available human research deserve as much attention as its findings.
The review examines observational studies involving human participants alongside laboratory experiments using human-derived gut microorganisms. Unlike the animal studies, the human research has not demonstrated consistent changes in overall microbiome composition associated with glyphosate exposure.
One study involving 130 twins detected glyphosate in the urine of approximately 53% of participants. Although researchers observed some differences in bacterial species richness, they did not identify consistent changes across several broader measures of microbial diversity.
These findings are relevant, but they also illustrate the difficulties of investigating microbiome effects in human populations. Diet, medication, environmental exposures and individual differences can all influence intestinal bacteria, making it difficult to isolate the contribution of any single chemical.
There is also an important distinction between measuring the overall composition of the microbiome and investigating what its microorganisms are actually doing. Changes in microbial metabolism or the activity of particular bacterial populations may not necessarily be reflected in broad measures of microbial diversity.
The review acknowledges that the available human evidence is predominantly null or inconclusive. It does not establish that typical dietary or environmental glyphosate exposure causes adverse microbiome effects or associated disease in humans.
But that leaves an important question unanswered: have human studies investigated the relevant biological effects, at appropriate exposure levels and over sufficient periods, to provide meaningful reassurance?
The animal evidence cannot simply be extrapolated to humans. Equally, limited or inconclusive human findings cannot resolve questions that existing studies were not designed or sufficiently equipped to answer.
For regulators, the challenge is not to assume that experimental findings necessarily translate into human harm. It is to determine whether those findings identify potential effects that warrant further investigation, particularly when they involve biological systems not routinely examined in conventional toxicity studies.
What Does This Mean for New Zealand?
For New Zealand, this review raises questions about whether the scientific evidence underpinning glyphosate’s continued approval adequately reflects what researchers now understand about its biological effects.
In July 2024, the Environmental Protection Authority (EPA) determined that the information submitted in support of reassessment did not meet the statutory criteria for significant new information and therefore did not establish grounds to reassess glyphosate and glyphosate-containing substances. Yet scientific research continues to investigate effects that extend beyond glyphosate’s original mode of action in plants, including interactions with the microorganisms living inside mammals.
The gut microbiome is not a minor consideration. Its microorganisms contribute to digestion, metabolism, immune regulation and the maintenance of the intestinal barrier. Experimental evidence that glyphosate and certain commercial formulations can alter these microbial communities raises questions about whether existing toxicological assessments sufficiently account for such effects.
If the original safety assessments did not adequately investigate the gut microbiome, how confidently can their conclusions be applied to this aspect of glyphosate exposure?
In earlier NMGNZ reporting, including Gut Check: What Glyphosate Is Doing to Your Microbiome, we explored concerns about glyphosate’s potential interactions with intestinal bacteria.
The new review provides an opportunity to revisit those concerns through a broader evaluation of the available evidence, including findings that support potential adverse effects and those that do not.
It also raises questions about the relationship between regulatory safety assessments and real-world exposure.
New Zealanders may encounter glyphosate residues through food and other environmental pathways. Our independent food testing programme has demonstrated that measurable residues can occur in everyday products, including bread, flour and honey.
The presence of glyphosate residues in food makes the question of exposure relevant to everyday life. Understanding the potential consequences requires examining not only how much glyphosate people encounter, but also which biological effects are considered when determining acceptable exposure levels.
If microbiome disruption is a relevant toxicological endpoint, were the studies underpinning existing exposure limits designed to detect it? Were commercial herbicide formulations examined alongside glyphosate alone? And were potential effects of repeated exposure during sensitive developmental periods adequately investigated?
These are questions that could be addressed through a transparent examination of the evidence used in New Zealand’s regulatory decisions.
The concern is not simply whether individual studies have demonstrated harm. It is whether the body of evidence used to justify continued approval adequately encompasses the biological effects that researchers are now investigating.
Without that examination, how can the public know whether existing regulatory assurances remain as comprehensive as the science requires?
A Scientific Review — Not a Final Verdict
This paper is a critical review of existing research rather than a new controlled experiment. Its conclusions depend on the quality, consistency and limitations of the studies it examines.
The review identifies important methodological weaknesses, including small study populations, differences in experimental diets, variations in microbiome measurement techniques and the difficulty of comparing results across animal models. It also acknowledges that the available human evidence remains limited and predominantly inconclusive.
Nevertheless, the authors identify a fundamental gap in conventional pesticide safety assessment: the gut microbiome is not incorporated into the standard regulatory toxicity battery.
Traditional guideline studies examine endpoints such as body weight, tissue abnormalities and clinical chemistry. They do not routinely measure changes in intestinal microbial communities or the substances those microorganisms produce. Consequently, a chemical could produce measurable changes in microbial composition or metabolism without those changes necessarily being identified through conventional toxicity testing.
The authors recommend incorporating microbiome and microbial-metabolite measurements into future regulatory studies, examining complete herbicide formulations and relevant chemical mixtures, and improving the evidence connecting animal experiments with human exposure.
The review does not establish that current exposure limits are unsafe. But it provides reasons to investigate whether the evidence used to establish those limits adequately addresses the effects now being identified in experimental research.
The review’s author, Robin Mesnage, has published extensively on glyphosate and glyphosate-based herbicides. The paper discloses his involvement as a consultant on glyphosate risk-assessment matters in US litigation. That relationship is relevant context, but the scientific value of the review ultimately depends on the strength of its evidence and reasoning.
Is the Absence of Evidence Still Reassuring?
The scientific understanding of glyphosate has evolved considerably since the herbicide was first introduced.
What began as an explanation centred on a biochemical pathway in plants now encompasses questions about microbial communities, commercial herbicide formulations, environmental mixtures and biological effects that may occur indirectly.
The absence of the shikimate pathway in mammalian cells remains a biological fact. But mammals are not composed solely of mammalian cells. They depend on complex communities of microorganisms, many of which possess the very pathway glyphosate was designed to inhibit.
That distinction challenges the completeness of one of the longstanding explanations for glyphosate’s apparent safety.
The new review brings together evidence that glyphosate and certain glyphosate-based herbicides can affect the mammalian gut microbiome under experimental conditions. It also identifies substantial gaps in understanding how those findings relate to human exposure and health.
Those gaps should not be treated as evidence that harm has occurred. But neither should they be mistaken for evidence that the questions have been resolved.
For New Zealand’s EPA, the issue is whether emerging scientific findings are being systematically evaluated against the evidence underpinning existing approvals, and whether that process is sufficiently transparent for the public to understand how decisions are reached.
The question is not whether every new study should trigger a reassessment. It is whether the cumulative evidence, including research into biological effects that may not have been adequately investigated in earlier assessments, warrants renewed scrutiny.
Glyphosate has been used for more than half a century. Our understanding of the microorganisms living inside us, and their importance to health, has developed enormously during that time.
If the scientific evidence is evolving, shouldn’t our assessment of safety evolve with it?
Image Source & Attribution
Feature image created using OpenAI’s AI image-generation technology and edited for publication using Canva. The image is an illustrative representation of the human digestive system and gut microbiome, not an actual scientific or medical image.
