The active ingredient in the popular weed killer Roundup, glyphosate, is the most widely used herbicide in the world. While it is known for killing weeds, a growing body of research suggests it may also be disrupting the human gut microbiome.
Roughly 90 percent of soybeans, corn, beets, and canola grown in the United States are farmed using glyphosate-resistant crops. This means the herbicide is sprayed directly on fields where food grows, and it can end up in water, crops, and the human body.
Glyphosate kills weeds by blocking a biochemical process that plants need to make certain nutrients. Because the human body does not use this same process, the chemical was long considered safe. However, many beneficial gut bacteria do rely on that process. In 2010, the company Monsanto was granted a patent on glyphosate as an antimicrobial agent, confirming its antibiotic properties.
Studies on the effects of glyphosate have accelerated in recent years. In one mouse study, animals exposed to low doses of glyphosate over 90 days showed significant shifts in their gut bacteria. Beneficial bacteria were reduced, while groups linked to gut dysbiosis and intestinal inflammation increased. Bacteria that produce butyrate, a fatty acid that supports gut lining repair, were depleted, as was the beneficial strain Bifidobacterium.
A systematic review in the journal Food & Function analyzed research across multiple animal models. The review found that glyphosate can disrupt gut bacteria, increase gut permeability (often called “leaky gut”), interfere with the protective mucus layer in the gut, and cause physical damage to the intestinal wall. The authors noted 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, it cannot be washed off.
Generational Concerns
Research on prenatal glyphosate exposure in mice examined doses as low as 0.01 mg/kg/day, which is 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 (a key component of the gut’s protective mucus layer), and pro-inflammatory cytokine profiles in both first- and second-generation offspring.
Behavioral deficits were also observed in the study, including reduced locomotion and impaired working memory. The bacterium Akkermansia muciniphila, which is linked to gut barrier integrity and metabolic health, was depleted in exposed animals.
The Gut-Brain Connection
The microbiome communicates directly with the brain via the gut-brain axis, a network that influences mood, cognition, and neurological health. When glyphosate disrupts the microbiome, the effects may extend beyond the gut. Beneficial species like Lactobacillus and Bifidobacterium, both sensitive to glyphosate, are considered psychobiotics because they have measurable effects on mood and cognition.
The prenatal exposure study added further weight to this concern, as glyphosate-exposed mice showed reduced serum kynurenine, a precursor to neuroactive metabolites, along with molecular markers of enteric neuroinflammation.
Completely eliminating glyphosate exposure is not realistic, but there are steps people can take to protect their microbiome. Choosing organic versions of high-risk crops such as oats, legumes, soy, corn, and wheat can meaningfully reduce dietary exposure. Certified organic farmers are prohibited from using glyphosate.
Filtering tap water with a high-quality activated carbon filter can reduce glyphosate levels in drinking water. Eating more fermented foods, such as organic sauerkraut, kimchi, or kefir, can help restore microbial diversity, as some fermented foods can break down glyphosate. The fungus used to ferment miso and soy sauce has also been shown to break down the herbicide. Eating fiber feeds the beneficial bacteria that glyphosate depletes, helping to build microbiome resilience.
