Do Herbicides Affect My Gut Health?

Do Herbicides Affect My Gut Health?

Published on Monday, November 28, 2022 by Emily Hamm

There is a lot of talk surrounding pesticides/herbicides and the agricultural business. 

Many organizations and influencers encourage shoppers to buy organically grown produce and grains to help reduce the number and type of herbicides/pesticides used on these crops.

Glyphosate is an herbicide (found in Roundup) that has received a lot of attention surrounding claims that it is harmful to human health. In regards to the gut microbiome and gut health, there are still many questions surrounding glyphosate and its effects on humans. Several animal and cell studies have been conducted with inconsistent and contradictory findings. 

Let us dig a little deeper.

What is glyphosate?

It is an herbicide frequently sprayed on cereal to accelerate the ripening process and facilitate the drying of the grain. It also acts on weeds during the cultivation process for Roundup-tolerant genetically modified crops.

o   Found heavily on oats, barley, and a variety of beans

How does it work?

It acts on plants by preventing the binding of phosphoenolpyruvate (PEP) which is a substrate to the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) which is an enzyme. This is a part of the shikimate pathway (a metabolic pathway in plants). It causes a shortage in aromatic amino acid production and leads to the death of the plant which it is targeting.

How is this a proposed problem for the gut?

Some strains of fungi and bacteria that are in the gut consist of a shikimate pathway and it is proposed that glyphosate may interfere with these gut microbes causing shifts in the bacteria profile which could in turn lead to gut dysbiosis or an imbalance of the gut microbiome.

What does research suggest?

study assessed the effects of glyphosate on the gut microbiome of rats. They found that glyphosate exposure inhibited EPSPS binding of the shikimate pathway of the gut microbiome in rats. However, the gut microbiome of rats and humans is vastly different so it is difficult to interpret these results regarding the human gut microbiome.

It is known that a variety of chemical pollutants and residues may interfere with the metabolic, endocrine, and neurodevelopmental paths linked to the gut microbiome. And specifically in infants and young children, this could be aggravated due to their developing microbiomes

recent study using SHIME technology (a new technology for research that mimics the entire human gastrointestinal tract- WOW) studied the effects of glyphosate (isolated) and Roundup (glyphosate-based herbicide) on the activity and composition of the gut microbiome from a feces sample of a 3-year-old human. Below is a summary of the findings and possible implications. It is important to remember that this design is very limited and conclusions cannot be made from one sample.

  • Change in the fermentation of the gut microbiome after roundup exposure- increased levels of lactate and acetate. Bacteria that tolerate a lower pH were increased like lactobacilli. There was an overall decrease in butyrate-producing bacteria which could lead to a shift in gut homeostasis resulting in dysbiosis
  •  Lower alpha diversity – which in early childhood has been correlated to lower cognitive ability, type 1 diabetes, and asthma
  • Roundup resulted in an increase in firmicutes to bacteroidetes ratio while glyphosate alone reduced this ratio

So overall, when it comes to the effects of herbicides on the human gut, more information is needed. In the meantime, follow your gut instinct (HaHa pun intended) and buy what you feel is right for you and your family in regards to organic vs non-organic. Make sure to always wash your produce well under warm water and wipe off dirt or residue that remains. Click here to learn more about organic produce.


  1. Environmental Protection Agency. (n.d.). EPA. Retrieved October 30, 2022, from
  2. Mayo Foundation for Medical Education and Research. (2022, April 22). Are Organic Foods Worth the price? Mayo Clinic. Retrieved October 29, 2022, from
  3. Mesnage, R., & Antoniou, M. N. (2020). Computational modeling provides insight into the effects of glyphosate on the shikimate pathway in the human gut microbiome. Current Research in Toxicology, 1, 25–33.
  4. Puigbò, P., Leino, L. I., Rainio, M. J., Saikkonen, K., Saloniemi, I., & Helander, M. (2022). Does Glyphosate Affect the Human Microbiota?. Life (Basel, Switzerland), 12(5), 707. 
  5. Mesnage, R., Calatayud, M., Duysburgh, C., Marzorati, M., & Antoniou, M. N. (2021). Alterations in human gut microbiome composition and metabolism after exposure to glyphosate and roundup and/or a spore-based formulation using the Shime® Technology.
  6. Mesnage, R., Teixeira, M., Mandrioli, D., Falcioni, L., Ducarmon, Q. R., Zwittink, R. D., Mazzacuva, F., Caldwell, A., Halket, J., Amiel, C., Panoff, J.-M., Belpoggi, F., & Antoniou, M. N. (2021). Use of shotgun metagenomics and metabolomics to evaluate the impact of glyphosate or Roundup Mon 52276 on the gut microbiota and serum metabolome of Sprague-Dawley Rats. Environmental Health Perspectives, 129(1), 017005. 

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