Living Well & Understanding the Body:

Pesticide Use & the Gut Microbiome

Global Autoimmune Institute July 21, 2023

What Is the Gut Microbiome?

The gut microbiome refers to the microbes of the gut — the bacteria, fungi and viruses. There are up to 100 trillion microbes in the human intestine (1) — and bacteria species are the main component. 

The genes encoded by bacteria within the human gastrointestinal tract actually outnumber human genes by more than 100 times (2)!

Bacteria species – which are taxonomically classified by genus, family, order, and phyla – can play a variety of roles. 

While every gut microbiome is different due to an individual’s exercise and diet habits – among other factors – a healthy microbiota composition enables metabolic and immune functions to perform optimally. An imbalance of gut microbiota, on the other hand, has been linked to intestinal diseases like irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD).

How Do Pesticides Impact the Human Gut Microbiome?

Pesticides have become a key part of agricultural production because their use can lead to greater crop yields. But pesticides intended to control weeds and pests can ultimately reach the soil, water, air, and food, negatively affecting humans. The gut microbiome metabolizes chemicals, but pesticides can impair its activity and composition. The gastrointestinal tract — which is a barrier against pathogenic microorganisms and toxins — is a key site for exposure. 

“Many factors influence the gut microbiome, including diet, such as ultra-processed food, as well as medications, illness, environmental chemicals such as pesticides, and hormones,” said Karen Costenbader, a physician specializing in rheumatology at Brigham and Women’s Hospital.

Costenbader and others have determined that in addition to added chemicals in one’s diet, pesticides are another exposure that research shows may increase the risk of developing an autoimmune disease. However, it is still not completely clear how pesticides interact with the microbiome and what effects the interaction has on human health.


Which Autoimmune Diseases are Specifically Impacted by Pesticides?

Pesticides and insecticides have been found to influence autoimmune hepatitis (AIH), systemic sclerosis (SSc), inflammatory bowel disease (which includes Crohn’s disease and ulcerative colitis), systemic lupus erythematosus (SLE), and rheumatoid arthritis (RA), (3) among other ADs. Multiple Sclerosis (MS), Crohn’s Disease and thyroid diseases have also been associated with pesticide exposure.


Vojdani, A.; Vojdani, E. The Role of Exposomes in the Pathophysiology of Autoimmune Diseases I: Toxic Chemicals and Food. Pathophysiology 2021, 28, 513-543.

A multitude of studies have examined the role that environmental factors play in the pathogenesis of autoimmune diseases. In patients with SLE, for example, exposure to pesticides in rural areas resulted in more than 3.5 times more oxidative DNA damage compared to exposure among those living in a city (4). Researchers have also found an association between insecticide use and RA and SLE among groups of post-menopausal women and farmers — with more exposure associated with a higher risk of developing disease. Lupus may have origins in abnormal lymphocyte functions. 

“It is plausible to think that pesticides could damage genes that are important to lymphocyte function,”

said Costenbader. But research can be complicated because the research available is often based on data using small population sizes. It’s also difficult to isolate one agricultural exposure or to look specifically at a single pesticide as the cause of an autoimmune disease. “It can be challenging to rule out biases and prove causality in observational settings,” said Christine Parks, a staff scientist at the National Institute of Environmental Health Sciences. “There’s a lot of work to be done.”

Which Pesticides Are the Major Culprits?

Pesticides include a wide variety of chemicals such as herbicides, insecticides, and fumigants that are used in the home and in farming. Some, like DDT, are no longer in use but may still be circulating in people’s blood systems. Others are easy to purchase and less acutely toxic.  

“You have herbicides to treat the weeds, and then insecticides, and then among each one of those, you have dozens of different types of chemicals and products that are used,” said Parks. Although pesticide use is associated with autoimmune diseases, the role of specific pesticides in the development of systemic autoimmunity is not entirely established. Certain organochlorine insecticides are associated with an increased risk for ADs (5). Exposure to chlordecone, an organochlorine that was previously used widely to control rust mites, wireworms, crickets, and other bugs, for example, has been noted to accelerate the appearance of SLE. Crystalline silica has also been linked with an increased incidence of systemic autoimmune diseases, such as SLE, rheumatoid arthritis, and scleroderma. Chemicals kill insects by impacting their nervous system. 

How would an herbicide promote the development of an autoimmune disease?

“A pesticide that disturbs the immune response may help it go off balance in the context of another exposure which reveals an autoantigen. And the cycle develops into a clinically apparent disease,” explained Parks. 

How Can You Improve Your Gut Microbiome?

There’s wide interest in the relationship between autoimmune diseases and composition of the microbiome. While much remains unknown, every person has a distinct gut microbiome, and diet plays a key role. Some methods of improving the microbiome may include: 

    • Vegetarian diets may be beneficial for establishing a diverse and stable microbiome. Plant-based diets can also “promote effective intestinal immune responses, maintain intestinal barrier function, and protect against pathogens (6).”
    • Artificial sweeteners such as saccharin, sucralose, and stevia may adversely change the composition of the gut microbiota. When possible, use substitutes such as honey (7).
    • Foods containing prebiotics promote good bacteria, including garlic, onions, leeks, asparagus, artichokes, dandelion greens, bananas, seaweed, and beans (8).
    • A high-fiber diet affects the type and amount of microbiota in the intestines. That’s because short-chain fatty acids (SCFA) are released as a result of fermentation that occurs when dietary fiber is broken down, resulting in better microbial diversity. High-fiber foods include whole grains like wheat, oats, and barley (9).
    • Probiotic foods may further improve the microbiome because they contain beneficial, live microbiota. Some recommend fermented foods like kefir, yogurt with live active cultures, pickled vegetables, tempeh, kombucha tea, kimchi, miso, and sauerkraut (8).
    • Polyphenols, or secondary metabolites of plants, may increase beneficial bacteria in the gut microbiota. Polyphenols are present in fruit, vegetables, and plant-derived foods such as cocoa, chocolate, tea, coffee, and wine (10).

Elimination/Exclusion Diets

  • Autoimmune Protocol (AIP)
    • An extension of the Paleolithic diet, the AIP involves the elimination of foods that may act as antigens, stimulate mucosal inflammation, and/or trigger dysbiosis within the gastrointestinal tract (11) (12).
  • Specific Carbohydrate Diet (SCD)
    • The SCD is commonly used in the treatment of inflammatory bowel disease (IBD) by patients, and anecdotal evidence suggests it may be an effective for treatment of Crohn’s disease (CD) or ulcerative colitis (UC). The SCD is thought to be effective due to the increased bacterial diversity of the microbiome (13).
  • Low FODMAP Diet
    • A low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet is frequently used to manage symptoms of irritable bowel syndrome (IBS). However, a recent study showed that while “a low FODMAP diet consistently led to lower abundance of Bifidobacteria, there were no clear effects on diversity of the microbiome or abundances of other specific taxa” (14).
  • Mediterranean Diet
    • The Mediterranean diet may modulate gastrointestinal microbiota and reduce metabolic endotoxemia (the presence of too many lipopolysaccharides in the blood, which are toxins that reside on the outer membrane of bacteria that would otherwise not be allowed into our bloodstream) (15) (16).


  1. Article Sources
    1. Giambo, F., Teodoro, M., et al. (2021, May 21). Toxicology and microbiota: How do pesticides influence Gut Microbiota? A Review. International Journal of environmental research and public health. Retrieved from  

    2. Bull, M. J., & Plummer, N. T. (2014, December). Part 1: The human gut microbiome in health and disease. Integrative medicine (Encinitas, Calif.). Retrieved from 

    3. Chittrakul, J., et al. (2022, April 21). Pesticide exposure and risk of rheumatoid arthritis: A systematic review and meta-analysis. Toxics. Retrieved from 

    4. Khan, M. F., & Wang, H. (2020, January 10). Environmental exposures and autoimmune diseases: Contribution of gut microbiome. Frontiers in immunology. Retrieved from 

    5. Parks, C. G., et al. (2019, July 11). Lifetime pesticide use and antinuclear antibodies in male farmers from the Agricultural Health Study. Frontiers in immunology. Retrieved from 

    6. Wei Xiao, Qingsong Zhang, Leilei Yu, Fengwei Tian, Wei Chen, Qixiao Zhai. (2022). Effects of vegetarian diet-associated nutrients on gut microbiota and intestinal physiology. Food Science and Human Wellness. Retrieved from

    7. Ruiz-Ojeda, F. J., et al. (2019, January 10). Effects of sweeteners on the gut microbiota: A Review of Experimental Studies and Clinical Trials. Advances in nutrition (Bethesda, Md.). Retrieved from 

    8. The microbiome. The Nutrition Source. (2022, July 25). Retrieved from 

    9. Cronin, P., et al. (2021, May 13). Dietary fibre modulates the gut microbiota. Nutrients. Retrieved from 

    10. Correa, T. A. et al. (2019, December 20). The two-way polyphenols-microbiota interactions and their effects on obesity and related metabolic diseases. Frontiers. Retrieved from 

    11. Chandrasekaran, A., Molparia, B., Akhtar, E., Wang, X., Lewis, J. D., Chang, J. T., Oliveira, G., Torkamani, A., & Konijeti, G. G. (2019). The autoimmune protocol diet modifies intestinal RNA expression in inflammatory bowel disease. Crohn’s & Colitis 360, 1(3).

    12. Konijeti, G. G., Kim, N., Lewis, J. D., Groven, S., Chandrasekaran, A., Grandhe, S., Diamant, C., Singh, E., Oliveira, G., Wang, X., Molparia, B., & Torkamani, A. (2017, September 29). Efficacy of the autoimmune protocol diet for inflammatory bowel disease. Inflammatory Bowel Diseases, 23(11), 2054–2060.

    13. Kakodkar, S., Mikolaitis, S., Engen, P., & Mutlu, E. (2013). The bacterial microbiome of IBD patients on the specific carbohydrate diet (SCD). American Journal of Gastroenterology, 108.

    14. So, D., Loughman, A., & Staudacher, H. M. (2022). Effects of a low fodmap diet on the colonic microbiome in Irritable bowel syndrome: A systematic review with meta-analysis. The American Journal of Clinical Nutrition, 116(4), 943–952.

    15. Bailey, M. A., & Holscher, H. D. (2018). Microbiome-mediated effects of the Mediterranean diet on inflammation. Advances in Nutrition, 9(3), 193–206.

    16. Ghosh, T. S., et al. (2020). Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut69(7), 1218–1228.