Glyphosate, the active ingredient in the weed killer Roundup, is the most widely used herbicide in the world. New research suggests it may be quietly disrupting one of the body’s most important health systems: the gut microbiome.
Roughly 90 percent of soybeans, corn, beets, and canola grown in the United States are farmed using glyphosate-resistant crops. The herbicide is sprayed directly on fields where food grows, and it ends up in water, crops, and human bodies.
How Glyphosate Works and Why Gut Bacteria Care
Glyphosate kills weeds by blocking a biochemical process that plants use to make certain essential nutrients. Because human bodies do not use this same process, the chemical was long considered safe for people. However, a wide range of gut bacteria depend on that same process, including many beneficial species that keep people healthy.
In 2010, Monsanto was granted a patent on glyphosate as an antimicrobial agent. The most widely used herbicide in the world is also officially an antibiotic. Like any antibiotic, it does not discriminate between microbes that should be eliminated and those needed for survival.
What the Research Shows
Science on glyphosate and the gut microbiome has accelerated in recent years. In one mouse study, animals exposed to low doses of glyphosate over 90 days showed significant shifts in gut bacteria. Beneficial bacteria were reduced while groups linked to gut dysbiosis and intestinal inflammation increased.
Bacteria that produce butyrate, a short-chain fatty acid that supports gut lining repair and immune regulation, were depleted. So was Bifidobacterium, one of the most well-known beneficial strains. A systematic review in the journal Food & Function found that glyphosate can disrupt gut bacteria, increase gut permeability, interfere with the mucus layer that protects the gut lining, and cause physical damage to the intestinal wall. The authors noted that these changes have been linked to conditions including Crohn’s disease and Alzheimer’s disease.
Some farmers also use glyphosate as a desiccant, spraying it on crops like oats, chickpeas, lentils, and beans just before harvest to dry them out. Because these crops absorb the herbicide directly, the glyphosate cannot be washed off.
The Generational Concern
Research on prenatal glyphosate exposure in mice examined doses as low as 0.01 mg/kg/day, more than 100 times below the EPA’s acceptable daily intake. Even at that low dose, the study found disruptions in metabolic, immune, and behavioral markers that persisted into the second generation of offspring.
The findings included goblet cell depletion, reduced mucin-2 expression, and pro-inflammatory cytokine profiles in both first- and second-generation offspring. Behavioral deficits were also observed, including reduced locomotion and impaired working memory. Akkermansia muciniphila, a bacterium closely linked to gut barrier integrity and metabolic health, was depleted in exposed animals, while bacteria associated with metabolic and neurological vulnerability were elevated.
The Gut-Brain Connection
The microbiome communicates directly with the brain via the gut-brain axis, a two-way network that influences mood, cognition, and neurological health. When glyphosate disrupts the microbiome, the downstream effects may extend beyond the gut.
Beneficial species like Lactobacillus and Bifidobacterium fall into a class of microbes called psychobiotics, which have measurable effects on mood and cognition when present in sufficient quantities. When these populations are depleted, the gut-brain axis loses some of its most important communicators. The prenatal exposure study showed that glyphosate-exposed mice had reduced serum kynurenine, a precursor to neuroactive metabolites, along with molecular markers of enteric neuroinflammation.
How to Protect the Microbiome
Completely eliminating glyphosate exposure is not realistic, but there are meaningful steps people can take. Certified organic farmers are prohibited from using glyphosate. Prioritizing organic versions of high-risk crops such as oats, legumes, soy, corn, and wheat can reduce dietary exposure.
High-quality activated carbon filters have been shown to reduce glyphosate levels in drinking water. Some fermented foods can break down glyphosate, and the live cultures in them help restore microbial diversity. The fungus used to ferment miso, sake, and soy sauce, Aspergillus oryzae, has been shown to break down glyphosate. Fiber feeds the beneficial bacteria that glyphosate depletes, and prioritizing gut-supporting foods can make a difference in microbiome resilience.
