Glyphosate And The Gut Microbiome

Written by Robin Saar, RVT, VTS and Katie Dahlhausen, PhD

Published on April 26, 2023

When we think of factors that influence the gut microbiome, diet probably comes up first. But nutrition aside, a host of other factors impact the microbiome as well, such as the chemicals used in the manufacturing of commercial pet food. Here we explore current research about the possible effects of glyphosate, one of the world's most widely used herbicides, on the microbes in the gut of pets.

Glyphosate - What Is It?

Glyphosate is an important component of an herbicide more commonly known as Roundup®. This herbicide is applied to plants and disrupts a specific pathway that allows bacteria, fungi, algae, and parasites to synthesize small protein molecules. This pathway, known as the shikimate pathway, does not exist in mammals. Therefore, glyphosate has been deemed Generally Recognized as Safe (GRAS) for both humans and pets. However, its patent dates back to 1974 when knowledge of the gut microbiome was minimal to non-existent.

Why Is Glyphosate Used

A fast growing world population of both humans and pets adds pressure to the agriculture industry to maximize the production of food products. Weed and pest control chemicals are sprayed over an entire crop to reduce the effects of invasive or undesirable plant growth or insect devastation. Glyphosate is one of the most commonly used herbicides throughout the world.

Are plants harmed by glyphosate? The agriculture industry relies, in part, on genetic modification of plants to withstand exposure to glyphosate. Researchers continue to design genetically altered plants that can withstand exposure to chemicals, among other initiatives to maximize growth with limited resources.  

It’s these types of scientific endeavors that allow the agricultural industry to keep up with demand, which would be difficult to impossible to meet without them. However, it’s important to study the ramifications of such initiatives as well. In the case of glyphosate, researchers are learning that microorganisms in the gut may be negatively impacted.

Glyphosate Is Generally Recognized As Safe (Gras) For Ingredients In Pet Food, But What Does That Really Mean?

GRAS is regulated by the U.S. Environmental Protection Agency’s (EPA) and enforced by Food and Drug Administration (FDA), though the research to determine GRAS is completed by scientists outside of the FDA. Tolerance levels are established by the EPA to provide a “reasonable certainty of no harm.

Any ingredient in a diet must be considered safe for the pet. This includes dyes, preservatives, and nutrient components. This leads to the question: should the gut microbes be considered when determining what is Generally Recognized as Safe (GRAS) in pet foods? We know they are important for pet health, and we know they are affected by glyphosate.

The Effect of Glyphosate On Gut Microbiota

Glyphosate uses the shikimate pathway to inhibit the biosynthesis of proteins in their amino acid state. This is positive for pest control on crops, but not for the trillions of microbes that make up the gut microbiome. In 1974, when glyphosate was introduced, researchers didn’t know the intrinsic necessity of the functions of the gut microbiota to assist or complete physiological processes for the host.


The conglomeration of research from the last couple of decades identifies 3 potential ways that glyphosate could affect the gut microbes:

1) Toxicity through direct exposure. Direct exposure where the chemical is directly inhaled and orally ingested. Glyphosate has the potential to act as an antibiotic, killing both beneficial and harmful bacteria.

2) Toxicity through metabolic byproducts, like AMPA. The microbial metabolism of glyphosate results in the production of a toxic secondary metabolite, which has been identified in rat feces.

3) Disrupting the protective mucosal barrier of the intestinal wall. These changes can cause the intestinal barrier to be more sensitive to exogenous toxicants.

Important Studies

There are hundreds of studies that highlight the potentially harmful effects of glyphosate, including numerous ones specific to the impacts on the gut microbiome. There is evidence that

glyphosate exposure affects different genera of bacteria and that glyphosate exposure suppresses potentially beneficial microbes. Additionally, there is a link identified between direct exposure to pesticides, including glyphosate, with metabolic diseases, changes in reproductive and endocrine function, toxicity in the immune and neurological systems and some types of cancer.

Interestingly enough, there are also several studies that did not find that glyphosate altered the gut microbiomes of animals, from pigs to cows.  

What Does This Mean For Dogs And Cats?

While we know that direct exposure does negatively impact the gut microbiomes of pets, more research is needed to determine if residual glyphosate affects the gut microbiomes. Testing your patient’s gut microbiome is a good way to determine the health and balance of the microbes, and to monitor changes over time.

Research suggests that early and long-term exposure to glyphosate has a strong impact on gut microbiome composition, of which the long term effects have yet to be fully elucidated. The gut microbiome is a dynamic and modifiable ecosystem that is interconnected with nearly every aspect of host health.  

Pet parents looking to avoid products that may be exposed to glyphosate can choose organic individual ingredients or commercial diets that have been certified as organic.

Pets with complex diseases like chronic enteropathy or atopy may require additional therapies to reverse a dysbiotic state. Fecal Microbial Transplants (FMTs) provide thousands of species-specific microbes to restart normal functions in pets experiencing the symptoms of dysbiosis.

AnimalBiome’s FMT material comes from rigorously screened healthy dog and cat donors; the fecal microbes are lyophilized and conveniently provided in a loose powder. We offer a suite of FMT material for veterinary use, including enema material for fast-acting applications and as enteric-coated capsules (to protect viable microbes from acid in the upper GI tract).

Key Takeaways

  • Growing demand in the agricultural industry has encouraged the use of genetically modified plants to allow for the use of chemicals that disrupt the growth of pests to ensure maximum crop yield.

  • Glyphosate utilizes a specific pathway (shikimate pathway) which does not exist in mammals and was deemed Generally Recognized as Safe (GRAS) in 1974.

  • Glyphosate is known to be a bactericide and fungicide and has been shown to affect microbes in the gut in studies on rats and other species.

  • Diseases that are associated with glyphosate exposure include metabolic diseases, changes in reproductive and endocrine function, toxicity in the immune and neurological systems and some types of cancer. These conditions are also associated with gut dysbiosis.

  • Further research is needed to understand the residual effects of glyphosate on the gut microbiomes of dogs and cats.