Let me start with a number that tends to land with a thud. In CDC biomonitoring data from NHANES — the US National Health and Nutrition Examination Survey, the largest representative health study run in North America — glyphosate was detectable in the urine of around 80% of people tested. A separate analysis published in JAMA Internal Medicine found 87% of samples positive. These aren’t agricultural workers. These are the general American population, tested at random intervals between 1988 and 2016 — a period during which glyphosate use increased approximately fifteenfold.
UK data is thinner, but European biomonitoring studies tell a similar story. A 2013 study across 18 countries found glyphosate in the urine of 43% of participants, with UK prevalence among the higher end. The compound is in food, water, and air in ways that make meaningful avoidance difficult without knowing where your exposure is actually coming from.
None of this means it’s immediately dangerous at the concentrations most people carry. The question — the clinically relevant question — is what it does to the biological systems that govern how you feel and function. And for that, the shikimate pathway is where you need to start.
The Shikimate Pathway — Why You Should Care About Something Your Body Doesn’t Have
Glyphosate works as a herbicide by inhibiting an enzyme called EPSPS — 5-enolpyruvylshikimate-3-phosphate synthase — which is a critical step in the shikimate pathway. This pathway is used by plants, fungi, bacteria, and algae to synthesise aromatic amino acids: phenylalanine, tyrosine, and tryptophan. Animals don’t have the shikimate pathway, which is why glyphosate has been presented as essentially harmless to humans — we don’t use the pathway it blocks, so how can it affect us?
Here’s the problem with that argument: your gut bacteria do use it. And your gut bacteria are not incidental passengers. They produce vitamins, regulate immune signalling, manufacture short-chain fatty acids that feed your gut lining, synthesise neurotransmitter precursors, and maintain the competitive balance that prevents opportunistic organisms from establishing dominance.
Glyphosate doesn’t kill your gut bacteria directly. It selectively suppresses the shikimate-dependent species — which tend to be the beneficial ones — while leaving the species that don’t depend on the pathway largely unaffected. Which tend to be the problematic ones.
The species most sensitive to glyphosate include Lactobacillus and Bifidobacterium — the workhorses of a healthy microbiome — along with several Akkermansia strains associated with gut barrier integrity. The species more resistant to it include several Clostridia species, some Pseudomonas strains, and opportunistic pathogens that thrive when competition from beneficial organisms is reduced. This isn’t theory. It’s been demonstrated in multiple animal models and is increasingly supported in human microbiome data.
The net effect: chronic low-level glyphosate exposure can produce a microbiome shift that doesn’t show up as acute illness — no vomiting, no diarrhoea, nothing immediately attributable — but produces the slow background deterioration that manifests as dysbiosis on a GI-MAP, elevated inflammatory markers on blood chemistry, and the cluster of symptoms that brings people to functional medicine practitioners in the first place.
AMPA — The Metabolite That Tells You Something Additional
When glyphosate is metabolised — both in the environment and in the body — it breaks down into a compound called AMPA: aminomethylphosphonic acid. The glyphosate add-on to the OAT measures both glyphosate and AMPA, and the ratio between them matters clinically.
High glyphosate with low AMPA suggests recent or ongoing exposure that your body hasn’t had time to process — the input is still coming in. High AMPA relative to glyphosate suggests you’re processing existing exposure reasonably well, but the metabolic burden is present. High levels of both is the finding that warrants the most attention — sustained exposure with significant metabolic processing ongoing, which means detoxification pathways are engaged and potentially under strain.
AMPA itself has biological activity. It’s not simply a neutral breakdown product. Research has shown AMPA can disrupt cellular energy metabolism and has been found to be more toxic to some cell lines than glyphosate itself, though the human data here is still developing. What’s clear is that a test measuring glyphosate without AMPA is giving you half the picture at best.
Where the Exposure Is Actually Coming From
The obvious answer is food. Glyphosate is sprayed directly onto many crops — not just as a herbicide during growing, but as a desiccant on grain crops like oats, wheat, and barley immediately pre-harvest. This is the practice that produces some of the highest residue levels, because the crop is sprayed close to harvest with no time for residue reduction before consumption. It’s also the reason that oat products — including many considered “healthy” breakfast options — have consistently tested among the highest for glyphosate residue in independent analyses, including work by the Environmental Working Group in the US.
Beyond food, glyphosate has been detected in drinking water sources, in airborne particles near agricultural areas, and in household dust. Eating organic reduces exposure substantially but doesn’t eliminate it entirely, because glyphosate moves through water systems and soil in ways that don’t respect organic certification boundaries.
Highest exposure: Conventionally grown oats, wheat, barley and products made from them — bread, pasta, breakfast cereals, oat milk, beer. Pre-harvest desiccation means residues are often highest in these categories.
Moderate exposure: Conventionally grown legumes (lentils, chickpeas, soy), fruit and vegetables with systemic herbicide application, non-organic animal products from grain-fed animals.
Environmental: Drinking water in agricultural catchment areas, airborne residues, parks and public green spaces treated with glyphosate-based products.
Substantially lower: Certified organic food, filtered water (reverse osmosis removes glyphosate effectively), urban environments away from agricultural land.
Who Should Consider the Glyphosate Add-On
Not everyone. The add-on is £128 on top of the OAT cost, and like any test it should be ordered when the clinical picture suggests it will change what you do with the results. There are specific presentations where I think it’s worth doing.
Persistent dysbiosis that doesn’t fully resolve. If you’ve done the gut work — removed pathogens, repaired the barrier, re-inoculated with appropriate probiotics — and the GI-MAP still shows depressed Lactobacillus or Bifidobacterium, or you keep cycling back into the same dysbiotic pattern, glyphosate is worth ruling out as a maintaining factor. You can’t repopulate beneficial bacteria effectively if the environment they’re trying to live in is continuously hostile to them.
Elevated Clostridia markers on the OAT. HPHPA — the Clostridia metabolite that inhibits dopamine conversion — is one of the OAT findings I take most seriously. If this is elevated and gut work isn’t shifting it, glyphosate-driven suppression of the competitive organisms that normally keep Clostridia in check is a plausible mechanism worth investigating.
Agricultural or horticultural exposure. If you work in farming, market gardening, groundskeeping, or any role with direct herbicide contact, testing is essentially standard practice from my perspective. Occupational exposure is categorically different from dietary exposure.
Heavy conventional grain consumption. Someone eating conventional bread, pasta, oat porridge, and beer daily, without significant organic substitution, is carrying a meaningful dietary glyphosate load that adds up over years. If they’re also presenting with gut dysbiosis, inflammatory markers, or unexplained metabolic disruption, the add-on gives you data to work with.
Children with gut or neurodevelopmental presentations. I’m careful about claims in this area, but glyphosate’s effect on the shikimate pathway in gut bacteria — and therefore on tryptophan availability, serotonin synthesis, and gut-brain signalling — is a legitimate area of clinical interest in children with dysbiosis-associated presentations. I wouldn’t run this as a first test, but if the GI-MAP is showing significant dysbiosis in a child and conventional gut work isn’t resolving it, it’s worth considering.
What You Can Actually Do About It
Testing without a viable protocol is just expensive worry, so it’s worth being specific about what elevated glyphosate findings actually direct you toward.
The most impactful single intervention is dietary substitution of the highest-exposure foods. Switching from conventional oat products, bread, and pasta to certified organic equivalents removes the primary dietary input. This isn’t a permanent dietary restriction — it’s a reduction in ongoing load while the body clears existing accumulation and the gut microbiome rebalances.
Glyphosate binds to minerals — particularly manganese, zinc, and iron — via a process called chelation. This is part of its herbicidal mechanism (it starves plants of mineral cofactors). In the human gut, the same binding activity means that elevated glyphosate exposure is often accompanied by functional mineral deficiencies even when dietary intake is adequate. Checking manganese and zinc on blood chemistry, and ensuring mineral-rich food sources in the diet, is relevant alongside any dietary glyphosate reduction.
Supporting Phase II liver detoxification — specifically glutathione synthesis and sulphation pathways — helps process and excrete glyphosate and AMPA more efficiently. This means glycine (found in collagen, bone broth, and gelatinous cuts of meat), NAC, and cruciferous vegetables are all relevant. None of this is exotic or supplement-heavy — it’s the same detoxification support that appears across multiple OAT findings.
Finally, and most importantly: if glyphosate has been maintaining a dysbiotic environment, restoring the gut microbiome properly once exposure is reduced is the clinical priority. The GI-MAP gives you the baseline. The OAT tells you what the dysbiosis is producing metabolically. Reducing exposure, supporting mineral and detox status, and then running a targeted gut repair protocol in sequence — that’s the clinical order of operations.
The glyphosate add-on isn’t for everyone, and I’m not suggesting it should be routine. But it’s a clinically meaningful £128 in the right context — particularly when gut dysbiosis is proving resistant to standard interventions, when occupational or dietary exposure is significant, or when you want to rule out an environmental maintaining factor before concluding that a protocol has failed. The Organic Acids Test is already measuring the downstream consequences of gut dysbiosis. Adding glyphosate and AMPA gives you a direct window into one of the upstream causes.