Glyphosate, the active ingredient in the weed killer Roundup, 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, the community of trillions of microbes living in the digestive system.
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, eventually ending up in water, crops, and human bodies.
How Glyphosate Affects Gut Bacteria
Glyphosate kills weeds by blocking a biochemical process that plants use to make essential nutrients. Because the human body does not use this same process, the herbicide was long considered safe for people. However, a wide range of gut bacteria depend on that same process, including many beneficial species that help keep people healthy.
In 2010, Monsanto was granted a patent on glyphosate as an antimicrobial agent. This means the most widely used herbicide in the world is also officially an antibiotic. Like any antibiotic, it does not distinguish between harmful microbes and those needed for survival.
What Research Shows
Recent studies have examined glyphosate’s effects on the gut microbiome. 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. Bifidobacterium, one of the most well-known beneficial strains, was also reduced.
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 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.
Generational Concerns
Research on prenatal glyphosate exposure in mice examined doses as low as 0.01 mg/kg/day, which is the estimated Average American Diet level and 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, 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, both sensitive to glyphosate, fall into a class of microbes called psychobiotics. These 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 also found that glyphosate-exposed mice showed reduced serum kynurenine, a precursor to neuroactive metabolites, along with molecular markers of enteric neuroinflammation.
Protecting the Microbiome
Completely eliminating glyphosate exposure is not realistic, but there are steps that can be taken. Choosing organic versions of high-risk crops like oats, legumes, soy, corn, and wheat can reduce dietary exposure, as certified organic farmers are prohibited from using glyphosate.
Using high-quality activated carbon filters for tap water can reduce glyphosate levels in drinking water, especially for those living near agricultural land. Eating more fermented foods, such as organic sauerkraut, kimchi, or kefir, can help restore microbial diversity. Some fermented foods can also break down glyphosate.
The fungus used to ferment miso, sake, and soy sauce, Aspergillus oryzae, has been shown to break down glyphosate. Eating fiber also helps feed the beneficial bacteria that glyphosate depletes, supporting microbiome resilience.
Glyphosate was designed to kill plants, but the science increasingly shows it is also disrupting the microbial ecosystems inside humans. From gut imbalances and intestinal inflammation to potential effects on mood and future generations, the research paints a picture that deserves more attention.
