The Antibiotic You Were Never Prescribed But Are Taking Everyday

On glyphosate, psychobiotics, depleted soil, and why your gut health is an oncology question

Between 70 and 80 percent of American adults have detectable glyphosate in their urine. So do children as young as three. NHANES biomonitoring data from 2013 to 2018 confirms it. Glyphosate is now ambient in the food supply, in the water in agricultural communities, in the bodies of people who have never set foot on a farm.

Most people think of glyphosate as a weed killer. It is also a registered antibiotic. Monsanto received a patent for its antimicrobial properties in 2010. The shikimate pathway it targets exists in plants, but also in the microbes living in your gut. Every time you eat a residue of it, you are running a low-grade antibiotic course against your own microbiome. That would matter less if your gut microbiome were just a digestive footnote. It is not.

The Gut-Brain-Immune-And-Everything-Else Axis

Researchers Ted Dinan and John Cryan coined the term psychobiotic to describe specific microorganisms that, when consumed in adequate amounts, produce a measurable benefit to mental health. Certain gut bacteria synthesize GABA and serotonin precursors, communicate with the brain via the vagus nerve, produce short-chain fatty acids that cross the blood-brain barrier, and directly modulate immune tone. Disrupting that microbial ecosystem does not just affect digestion. It affects mood, cognition, anxiety, and stress response. The gut-brain axis is bidirectional, and it is exquisitely sensitive to what lives in the colon.

Glyphosate is not selective. It targets the shikimate pathway across all microbial species that use it, which includes many of the Lactobacillus and Bifidobacterium species that produce these neuroactive compounds. One study found that glyphosate damages more than half of the beneficial microbes in the human gut. Glyphosate-resistant bacteria that survive tend to be inflammatory strains. So the net effect of chronic low-level glyphosate exposure is a gut that skews toward dysbiosis, elevated systemic inflammation, and a progressively compromised gut-brain axis. A 2022 Canadian study found that glyphosate-resistant microbes may affect neurodevelopment, and that this altered microbial composition can be passed to subsequent generations.

The longevity space is saturated with wearables, peptides, NAD+ IVs, GLP-1s, rapamycin, CGMs, hyperbaric chambers, and cold plunges. But one of the cleaner signals keeps pointing back to something much simpler: prebiotics and probiotics, and specifically to Bifidobacterium. It is one of the organisms most consistently associated with healthy aging. Centenarian gut microbiome studies from Japan and Italy repeatedly show higher Bifidobacterium abundance compared to average elderly populations. It produces acetate, supports gut barrier integrity, synthesizes B vitamins, and keeps intestinal pH low enough to limit pathogen colonization. It also declines predictably with age under normal circumstances. Add chronic low-level glyphosate exposure to that trajectory and you accelerate a process that was already working against you. The gut-brain axis gets most of the press, but Bifidobacterium and its microbial neighbors are communicating with every major organ system: the liver through tryptophan and lipid metabolism, the heart through LDL modulation and cardiometabolic signaling, the kidney through oxidative stress pathways, and bone through osteoclast regulation and calcium signaling. Disrupting this ecology is not a localized problem.

Image from The role of Bifidobacterium in longevity and the future of probiotics https://doi.org/10.1007/s10068-024-01631-y

The Microbiome-Cancer Connection

The International Agency for Research on Cancer classified glyphosate as a probable human carcinogen in 2015. The strongest epidemiological signal has been for non-Hodgkin lymphoma, particularly diffuse large B-cell lymphoma, where pooled analyses of agricultural cohorts showed a meta-hazard ratio of approximately 1.36 (meaning people with occupational glyphosate exposure had a 36 percent higher rate of developing diffuse large B-cell lymphoma compared to unexposed people, pooled across multiple studies).

Image from Comprehensive assessment of pesticide use patterns and increased cancer risk https://doi.org/10.3389/fcacs.2024.1368086

More recent meta-analyses continue to show elevated risk in occupationally exposed populations, though the data from the Agricultural Health Study have been less consistent, which keeps this debate alive. A 2025 hypothesis paper in Environmental Sciences Europe raises another angle entirely: glyphosate may persist in bone, creating extended exposure to hematopoietic tissue that could explain some of the lymphoma signal.

The carcinogenicity question is important, but it is not the only reason oncologists should care about this. The deeper story is what a damaged microbiome does to cancer outcomes.

We now have substantial evidence that gut microbial diversity determines, in part, how well a patient responds to immune checkpoint inhibition. Patients with higher abundance of Akkermansia muciniphila and Ruminococcus species, and higher circulating short-chain fatty acids, show longer progression-free and overall survival on checkpoint inhibitors, particularly in melanoma and non-small-cell lung cancer. Butyrate, a fermentation byproduct, modulates PD-1 expression on CD8+ T cells, reducing exhaustion. Fecal microbiota transplant trials in checkpoint-refractory melanoma have achieved objective response rates of 20 to 40 percent in patients who had failed prior immunotherapy. That is really significant!

If you are eating a diet high in conventionally grown oats, lentils, chickpeas, and beans, you may be getting significant glyphosate exposure through desiccation. This is the practice of spraying Roundup on crops just before harvest to dry them uniformly for the combine. These crops absorb the herbicide. You cannot wash it off. The glyphosate lands in a gut that needs to be in optimal condition to run your immune system, and specifically to mount a cancer-fighting immune response.

It Starts in the Soil

The food is less nutritious than it used to be, independent of pesticide exposure. Industrial agricultural practices have depleted soil microbiomes and stripped mineral content from farmland. Magnesium levels in vegetables and wheat have declined by roughly 25 percent over the past several decades. Trace minerals including zinc, manganese, and copper have also fallen in measurable quantities. An estimated 50 percent of the population now has inadequate magnesium levels. Magnesium is required for over hundreds of enzymatic reactions, including DNA repair.

The soil microbiome and the gut microbiome are connected through the food we eat. Healthy soil produces microbe-rich, nutrient-dense food. Depleted soil, managed with synthetic inputs and herbicides that kill soil organisms, produces food that feeds neither you nor the microbes that protect you. Glyphosate degrades soil microbial communities directly. It compounds a problem that was already worsening.

What Can You Do

Testing

If you want to know your actual exposure level, urine testing is the standard method. The gold standard is LC-MS/MS (liquid chromatography-tandem mass spectrometry), which has 98 to 99 percent sensitivity and specificity and measures both glyphosate and its primary metabolite AMPA. Mosaic Diagnostics and US BioTek both offer urine-based testing that can be ordered through a clinician or functional medicine practitioner. ELISA-based tests are cheaper and more widely available but are prone to false positives and false negatives, I would not make clinical decisions based on an ELISA result alone. Collect a first-morning urine sample for the most concentrated reading, and be aware that a single negative result does not rule out chronic low-level exposure. Glyphosate's urinary half-life is roughly 5 to 12 hours in the rapid elimination phase, with over 90 percent cleared within 48 hours of exposure. Test within a day or two of a high-exposure meal and you may catch it; test a week later and you likely will not.

Detox protocol

There is no proven glyphosate detox protocol with high-quality human data behind it. What we have is mechanistic reasoning and a small amount of supportive evidence, which I think is enough to act on given the exposure burden, the known downstream risks and the interventions being low risk.

1. The first and most effective intervention is reducing exposure. Buy organic for oats, legumes, and grains whenever possible. These are the crops most likely to have been desiccated with glyphosate. For water filtration, reverse osmosis is the most effective option, removing up to 99% of glyphosate. High-quality coconut shell activated carbon can reach similar levels, but basic pitcher and fridge filters remove less than 20% and are not reliable for this purpose. An RO system with NSF/ANSI 58 certification combined with a carbon stage is the strongest home option.

2. Glycine supplementation: glyphosate is a structural analog of glycine and substitutes for it in proteins, causing misfolding. Flooding the system with glycine may competitively reduce that substitution and support renal clearance. The typical recommendation is 2 to 4 grams twice daily for a few weeks, then a lower (1 to 2 grams) maintenance dose.

3. Aspergillus oryzae, the fungus used in miso, sake, and soy sauce, has demonstrated capacity to biodegrade glyphosate. This is one of many reasons to increase fermented foods in the diet. Fermentation also degrades glyphosate in other contexts, and fermented foods introduce organisms that may help restore microbial diversity.

4. Fiber and ferments are foundational. Short-chain fatty acid producing organisms are the ones most vulnerable to antibiotic disruption and most critical to immune function and gut-brain signaling.

5. Activated charcoal is worth adding for patients with significant ongoing exposure. It adsorbs glyphosate in the gut before it can be absorbed — take it away from medications and food, or it will bind those too.

One System, Not Five

Glyphosate is engineered into 90 percent of conventional soy, corn, sugar beet, and canola in the US. It also reaches oats, wheat, lentils, chickpeas, dried beans, peas, and almonds through pre-harvest desiccation. Farmers spray it on these crops shortly before harvest to dry them uniformly, and it absorbs into the grain. The result is detectable glyphosate in nearly every American body tested. That exposure is chronic and low-grade, layered on top of soil depletion, ultra-processed food, and decades of routine antibiotic use, all of which push the microbiome in the same direction.

Photo by Hannah Shedrow on Unsplash

The organisms being depleted are the same ones modulating your neurochemistry, running your immune response, protecting your liver and kidneys, signaling your cardiovascular system, and tracking with healthy longevity in centenarian populations. Losing Bifidobacterium is not a minor digestive inconvenience. It is losing a key node in a network that reaches every major organ, and a major “longevity biohack.”

I believe the microbiome is one of the most underutilized levers in integrative oncology. The immunotherapy data alone (better survival outcomes, meaningful FMT responses in refractory disease) should make gut health a clinical priority for every cancer patient. Glyphosate is the thread connecting the soil depletion story, the mental health story, and the cancer story. The soil, the food, the gut, the brain, the immune system all run on the same underlying biology. Treating them in isolation is part of how we got here.

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Actionable takeaways

• Prioritize organic for oats, lentils, chickpeas, and beans These crops most often undergo glyphosate application

• Upgrade your water filtration to reverse osmosis; an NSF/ANSI 58-certified RO system with a carbon stage removes up to 99% of glyphosate

• Build a high-fiber, ferment-forward diet to protect and restore SCFA-producing organisms

• Take a Bifidobacterium-containing foods or probiotic. It is one of the clearest longevity signals in the microbiome literature and one of the first casualties of antibiotic disruption

• Consider glycine supplementation (2–4g twice daily for a few weeks) if your exposure has been high. It competes with glyphosate at the protein substitution level

• Eat miso, real fermented tofu, real soy sauce, and other Aspergillus-fermented foods regularly. The fungus degrades glyphosate and the ferment restores diversity

• Use activated charcoal short-term if exposure is significant; take it away from medications and food

• Consider urine glyphosate testing (LC-MS/MS via Mosaic Diagnostics or US BioTek) if you eat a conventional diet or live near agricultural land; test within 48 hours of a typical high-exposure meal for the most accurate read

• If you are an oncology patient heading toward immunotherapy, request a baseline gut microbiome assessment and address dysbiosis before treatment starts

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Ksenia Malarkey, ND is a naturopathic physician specializing in integrative oncology, hormones, and metabolic health.

She provides medical care for Washington residents and offers global health coaching.

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To schedule a free 15-minute consult, visit drkseniamalarkey.com