We’ve written before about the link between glyphosate and gluten sensitivity.
Now emerging research is identifying a specific biological mechanism — and it involves a group of bacteria most people have never heard of.
Something has been happening to human digestive health over the past four decades that genetics alone cannot explain.
Celiac disease — the autoimmune condition triggered by gluten, in which the immune system attacks the lining of the small intestine — affects approximately one percent of the New Zealand population — around 50,000 people. That sounds modest until you consider the trajectory: in Canterbury, the incidence of newly recognised celiac disease rose from 1.4 per 100,000 people per year in the early 1970s to 12.9 per 100,000 per year by the late 1990s — nearly a tenfold increase in three decades.
The authors of that study acknowledged that improved awareness, serological testing, and access to biopsy contributed to the rise. But diagnostic improvement alone cannot account for an increase of this magnitude — something environmental has also changed. Globally, the pattern is the same. A systematic review of fifty studies found a consistent, sustained rise in celiac disease incidence across geography, age, and sex that cannot be fully explained by improved diagnosis or increased awareness alone.
Genetics sets the stage for celiac disease — you need to carry certain gene variants to be susceptible. But genes do not change over four decades. Something environmental has changed. And for researchers willing to ask uncomfortable questions, one of the more plausible candidates keeps appearing in the data: glyphosate.
We have previously explored the broader connection between glyphosate and gluten sensitivity in our articles on glyphosate and gluten sensitivity, from gluten-free to glyphosate-free, and glyphosate and gluten intolerance. This piece goes deeper — into the specific biological mechanism that may connect glyphosate exposure to celiac disease risk, and why that mechanism deserves far more attention than it has received.
Meet Rothia: The Gut Bacteria That Degrade Gluten — and That Glyphosate May Be Destroying
The human gut contains trillions of microorganisms. Most people, if they think about gut health at all, think about general diversity — the idea that a richer, more varied microbial community is associated with better health. That is true. But the relationship between specific bacterial species and specific diseases is proving to be far more precise than that general picture suggests.
Enter Rothia — a genus of bacteria that inhabits the mouth, throat, and upper digestive tract, and which has, until recently, attracted relatively little scientific attention. That is changing.
Research has identified certain Rothia species as playing a critical and specific role in the degradation of gluten proteins. Gluten peptides — the fragments of wheat protein that trigger the immune response in celiac disease — are unusually resistant to digestion. The human body’s standard digestive enzymes, including those produced by the stomach, pancreas, and small intestine, struggle to break gluten down completely. The fragments that survive intact are the ones that provoke the autoimmune attack on the intestinal lining that defines celiac disease.
What certain Rothia species can do, in laboratory and animal studies, is produce enzymes capable of cleaving these otherwise resistant gluten peptides — breaking them down before they can trigger an immune response. Whether this translates to meaningful protection against gluten-related damage in humans remains under investigation, but the biological mechanism is established and plausible.
The question that follows is uncomfortable but important: what happens when Rothia populations are depleted?
How Glyphosate Disrupts the Gut Microbiome — and Why It Targets Beneficial Bacteria First
To understand the potential connection, it helps to understand how glyphosate affects the gut microbiome — and why it does not affect all bacteria equally.
Glyphosate kills plants by inhibiting an enzyme called EPSPS, which is part of the shikimate pathway — the biochemical route by which plants and many microorganisms synthesise essential aromatic amino acids. Mammals do not have the shikimate pathway, which is why glyphosate was long assumed to be essentially harmless to human biology. What this reasoning overlooked — and what the gut microbiome research has now firmly established — is that the trillions of bacteria living in the human gut do have the shikimate pathway. Glyphosate, when it reaches the gut after ingestion, acts on those bacteria through the same mechanism it uses to kill plants — inhibiting the shikimate pathway — with effects on gut microbial communities that some researchers have compared to those of a selective antibiotic.
But crucially, it does not act equally. Research has consistently found that glyphosate disproportionately suppresses the bacteria that are most beneficial to human health — including Lactobacillus, Bifidobacterium, and, critically, certain Rothia species — while leaving more resistant opportunistic pathogens relatively unaffected. The net effect is a shift in gut microbial community composition toward an inflammatory, dysbiotic state: fewer protective species, more pathobionts.
A 2020 peer-reviewed review by Barnett and Gibson at the University of British Columbia found that glyphosate residues could cause dysbiosis, and specifically identified Rothia population depletion as a concern. The authors suggested glyphosate may represent an environmental trigger in the development of celiac disease — while explicitly acknowledging that methodological weaknesses in the available research make it impossible to draw definitive conclusions about glyphosate’s effects on the microbiome and human health. That honest caveat should not obscure the significance of what the review identifies: a specific, plausible, peer-reviewed mechanism that warrants serious investigation and has not received it.
This is not a fringe hypothesis. It is a specific, mechanistically coherent pathway — glyphosate reduces Rothia → Rothia reduction impairs gluten degradation → incompletely degraded gluten peptides survive to trigger immune responses → in genetically susceptible individuals, celiac disease or gluten sensitivity develops or worsens. Each step in that chain is supported by research. The question of whether the full chain operates in humans, at real-world exposure levels, has simply not been adequately investigated.
Glyphosate in Your Bread and Cereal: How Pre-Harvest Spraying Puts Residues in Grain
There is a further dimension to this story that most New Zealanders are unaware of — and that significantly changes the calculus of exposure.
Glyphosate is not only used as a weed killer. For decades, it has also been used as a pre-harvest desiccant: sprayed directly onto wheat, oats, barley, and other grain crops in the weeks before harvest to dry them evenly and allow earlier, more convenient harvesting. This practice — sometimes called “crop ripening” — is common in countries with variable harvest weather, including Australia, the United Kingdom, and Canada, and was used in New Zealand until commercial pressure and regulatory action brought it to a halt.
In October 2025, MPI formally ruled that glyphosate on wheat, barley, and oats grown for human consumption may only be applied before crop emergence — effectively prohibiting direct pre-harvest application on those crops. That is a meaningful step. But it does not resolve the exposure question for several reasons.
First, the ban applies only to domestically grown grain destined for human consumption. Pre-harvest desiccation remains permitted on grain used for animal feed — and cross-contamination between feed and food grain in shared storage, transport, and processing facilities is a documented risk that has not been adequately addressed.
Second, and more significantly for the average New Zealand consumer: a substantial proportion of the grain products sold in New Zealand supermarkets — including breakfast cereals, flour, pasta, oat products, and bread — is imported from countries where pre-harvest desiccation remains standard practice. When glyphosate is used as a desiccant, it is applied directly to the grain at a stage when there is minimal time for the chemical to break down before harvest. Grain treated this way carries some of the highest glyphosate residue levels of any food product — far higher than residues found on crops where glyphosate was used only for weed control earlier in the growing season.
This means that for many New Zealanders, the primary dietary glyphosate exposure may not come from fresh produce or environmental contamination — it may come from imported bread, pasta, cereals, and oat-based products. These are precisely the foods that contain gluten. And they are the foods that, according to the Rothia research, may carry the very chemical that impairs the gut’s ability to degrade gluten safely.
The overlap is not coincidental. It is structural. Pre-harvest desiccation applies glyphosate to gluten-containing grains. That glyphosate, when consumed, has the potential to disrupt the Rothia populations that help degrade gluten in the gut. In genetically susceptible individuals — and approximately 30 to 40 percent of the population carries the genetic variants associated with celiac disease risk, even if only one percent develops full celiac disease — this disruption may be enough to tip the balance toward disease expression.
For more on New Zealand’s desiccation history and the 2025 regulatory decision, and on how glyphosate gets into our food, see our previous investigations.
Does Glyphosate Cause Celiac Disease? What the Evidence Does and Doesn’t Show
Before going further, it is worth being clear about what this research does and does not establish.
The original hypothesis linking glyphosate to celiac disease — advanced in a 2013 paper by Samsel and Seneff — was heavily criticised, and fairly so, for presenting correlations and theoretical mechanisms as if they constituted evidence of causation. The National Celiac Association and others have noted that large-scale epidemiological studies in humans have not confirmed a direct causal relationship between glyphosate exposure and celiac disease.
We are not making that claim here. What we are saying is something more specific and more defensible: the Rothia bacteria finding, supported by peer-reviewed research, provides a plausible biological mechanism through which glyphosate exposure could contribute to gluten sensitivity in susceptible individuals. That mechanism is worth taking seriously — particularly given the pre-harvest desiccation context, which creates a direct, concentrated route of glyphosate exposure via the exact foods that contain gluten.
There is also a phenomenon that the Rothia research may help explain: the growing number of people who report feeling better when they eliminate wheat from their diet, but who test negative for celiac disease and do not carry the classic celiac genetic markers. Non-celiac gluten sensitivity is a recognised clinical entity, but its mechanism is poorly understood.
If glyphosate is disrupting Rothia populations — impairing gluten degradation in the gut even in people who are not genetically predisposed to full celiac disease — it would produce exactly the pattern of symptoms that are increasingly being attributed to “gluten intolerance”: bloating, intestinal discomfort, fatigue, brain fog, and systemic inflammation. And it would explain why these symptoms resolve when people avoid wheat — not because wheat protein itself is the problem for these individuals, but because avoiding wheat means avoiding the glyphosate residues it carries.
Put another way: some people who think they are reacting to gluten may actually be reacting to what has been sprayed on the wheat. The implications are profound — for how we understand the apparent epidemic of gluten sensitivity, and for how we regulate the chemicals applied to our food supply.
The same concern applies closer to home — literally. New Zealanders who use glyphosate-based herbicides in their gardens, on driveways, or around the home without adequate protective equipment may be absorbing glyphosate through the skin, inhaling spray drift, or ingesting trace amounts through hand-to-mouth contact during or after application. Studies have detected glyphosate in the urine of home users and occupational sprayers, suggesting these non-dietary routes of exposure are real and measurable.
Whether glyphosate absorbed through these routes reaches the gut microbiome at concentrations sufficient to disrupt Rothia populations is not yet established — but it is a question that deserves serious investigation, particularly for people who spray regularly and without adequate protection.
Why Glyphosate Safety Testing Was Never Designed to Detect Gut Microbiome Harm
As we have documented in our investigation into why animal studies may be systematically underestimating glyphosate’s harm, the safety limits currently applied to glyphosate were not designed to account for gut microbiome effects. The standard toxicological testing framework looks at direct tissue damage, cancer risk, and organ toxicity. It does not assess the selective antibiotic effects of glyphosate on specific gut bacterial populations, or the downstream consequences of those effects for autoimmune disease risk.
This is the same structural testing gap we identified in our investigation into glyphosate and Parkinson’s disease — where we found that current regulatory neurotoxicity testing cannot detect the slow, progressive damage that produces Parkinson’s, and that the gut-brain axis may be the very mechanism by which glyphosate’s neurological effects are mediated. The gut microbiome sits at the intersection of both stories: potentially connecting glyphosate exposure to celiac disease on one hand, and to neurodegeneration on the other.
MPI and New Zealand’s EPA set glyphosate residue limits for wheat and grain products based on safety assessments that predate the Rothia research and do not account for the specific microbiome disruption pathway it identifies. While MPI’s October 2025 decision to restrict glyphosate application on domestic grain for human consumption to pre-emergence only is a step forward, the residue limits themselves — and the safety assessment framework underpinning them — remain unchanged. Imported grain products, which make up a significant proportion of what New Zealanders eat, are still assessed against these same limits, under a framework that was never designed to evaluate gut microbiome effects.
Is Gluten the Problem — or Is It the Glyphosate Sprayed on the Wheat?
For the growing number of New Zealanders who have eliminated wheat from their diets — either because they have been diagnosed with celiac disease, or because they have found that avoiding gluten makes them feel better — the Rothia research raises a question worth sitting with.
If the protective bacteria that help degrade gluten in the gut are being selectively suppressed by a herbicide that is applied directly to wheat before harvest — whether that wheat is grown overseas and imported, or grown domestically for animal feed — then the problem is not gluten. The problem may be what is done to the wheat — and the system that continues to permit it.
A strict gluten-free diet is currently the only effective treatment for celiac disease. It works. But it is a response to a symptom, not an investigation of a cause. If glyphosate’s disruption of Rothia populations is contributing to the inability to tolerate gluten — either by failing to degrade gluten peptides adequately, or by creating an inflammatory gut environment in which those peptides are more likely to trigger an immune response — then removing gluten addresses the downstream consequence while leaving the upstream cause untouched.
The autoimmune damage caused by gluten exposure in people with the condition is real, serious, and well-established. This article does not challenge that. But we are in a position to ask: is the research into what is causing the rise in celiac disease keeping pace with the research into how to manage it? And is the regulatory framework governing what is sprayed on our grain crops keeping pace with what the gut microbiome research is revealing?
The Rothia finding is not proof. But it is a signal — specific, mechanistically coherent, and consistent with the broader pattern of evidence linking glyphosate to gut microbiome disruption. In the face of a rising autoimmune condition affecting one percent of the New Zealand population, with incidence that cannot be explained by genetics or diagnosis rates alone, that signal deserves more than silence from the agencies responsible for food safety.
This article is part of an ongoing investigation into glyphosate’s effects on human health. We encourage readers to consult the primary sources and form their own conclusions.
Further Reading
On glyphosate, Rothia bacteria, and celiac disease
- Barnett, J.A. & Gibson, D.L. (2020). Separating the empirical wheat from the pseudoscientific chaff: a critical review of the literature surrounding glyphosate, dysbiosis and wheat-sensitivity. Frontiers in Microbiology, 11, 556729. ncbi.nlm.nih.gov — The key peer-reviewed review identifying Rothia bacteria depletion as a plausible mechanism connecting glyphosate exposure to celiac disease and gluten sensitivity.
- Samsel, A. & Seneff, S. (2013). Glyphosate, pathways to modern diseases II: Celiac sprue and gluten intolerance. Interdisciplinary Toxicology, 6(4), 159–184. ncbi.nlm.nih.gov — The original paper proposing the glyphosate-celiac connection. Controversial and criticised for overstating causation, but its mechanistic framework has informed subsequent research.
- Walsh, L., Hill, C. & Ross, R.P. (2023). Impact of glyphosate on the composition and functionality of the gut microbiome. Gut Microbes. ncbi.nlm.nih.gov — Comprehensive peer-reviewed review of glyphosate’s documented effects on gut microbial communities.
- The Detox Project (2023). Wheat Intolerance Might Be Due to Glyphosate — New Study. detoxproject.org — Accessible summary of the Barnett and Gibson research and its implications for wheat sensitivity.
On celiac disease prevalence in New Zealand
- Cook, B. et al. (2004). A thirty-year (1970–1999) study of coeliac disease in the Canterbury region of New Zealand. NZ Medical Journal, 117(1189). pubmed.ncbi.nlm.nih.gov — The primary NZ longitudinal data showing the near-tenfold rise in celiac disease incidence over three decades.
- Coeliac New Zealand. The Clinical Presentation of CD is Changing. coeliac.org.nz — Overview of changing celiac disease patterns in NZ including incidence data.
On glyphosate pre-harvest desiccation and grain residues
- Barnett, J.A. et al. (2023). Pre-natal glyphosate exposure induces dysbiosis, metabolic dysfunction and behavioural abnormalities three generations after exposure. Journal of the Canadian Association of Gastroenterology. ncbi.nlm.nih.gov — Multi-generational effects of glyphosate exposure via dietary routes including pre-harvest desiccation.
- MPI (October 2025). Glyphosate residue limits to stay at 0.1mg/kg for wheat, barley and oats, with restrictions introduced on permitted use. mpi.govt.nz — The formal NZ regulatory decision restricting glyphosate on wheat, barley, and oats for human consumption to pre-emergence application only.
- No More Glyphosate NZ. NZ Glyphosate Submissions: What Really Changed. nomoreglyphosate.nz — Analysis of the October 2025 MPI decision including remaining loopholes.
- No More Glyphosate NZ. How Glyphosate Gets Into Our Food. nomoreglyphosate.nz — Detailed explanation of the desiccation practice and its residue implications for NZ consumers.
Related NMGNZ investigations
- No More Glyphosate NZ. Glyphosate and Gluten Sensitivity. nomoreglyphosate.nz
- No More Glyphosate NZ. From Gluten-Free to Glyphosate-Free. nomoreglyphosate.nz
- No More Glyphosate NZ. Glyphosate and Gluten Intolerance. nomoreglyphosate.nz
- No More Glyphosate NZ. Is Glyphosate Really Safe? Why the Animal Studies Say Less Than You Think. nomoreglyphosate.nz
- No More Glyphosate NZ. Glyphosate and Parkinson’s Disease: Is New Zealand Asking the Right Questions? nomoreglyphosate.nz
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