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The Microbiome and The GMO Debate

With the Right to Know initiative on the upcoming Oregon ballot, I thought it might be a relevant time to address some of the potential relationships between genetically modified organisms (GMOs) and the human gut microbiome. This post details the relationship between GMOs and the human gut microbiome. In a future post I will go into more depth about my personal issues with the use of transgenic plants for food crops, which are primarily related to environmental impacts.

Arguments against the production and consumption of genetically modified food crops are plentiful. Most revolve around problems with the genetic modification process, potential allergen cross-contamination, and possible impacts genetic modification of food crops on our bodies and the environment. All of these things are worth further exploration. I sometimes have people ask me why I choose not to eat GMO foods, given that they haven’t been proven to be dangerous. My answer is this: I don’t know for sure that these foods are safe, and I have other safe, and probably healthier, options available. It is not a risk I am willing to take. On top of that, as an environmentalist, I cannot condone farming practices that are not only detrimental to the soil, but that, by their very nature, dump exponentially larger quantities of toxins into the ecosystem than any organic farming operation would.

Far and away the biggest concern for me, however, is the fact that most crops are being genetically modified solely so that more pesticides and herbicides (see Roundup) can be added to crops without killing them. What this means is that GMO food crops are very often drenched in these chemicals that are meant to kill other living organisms. On top of that, there is evidence that roundup-ready crops are not only resistant to the herbicide effects, but they also appear to absorb more of the herbicide than non-GMO crops. Research increasingly indicates that the high concentration of pesticides and herbicides in our food system might be causing some serious negative health effects.

A huge amount of genetic modification of food crops is performed for the purpose of increasing the use of herbicides and pesticides. Roundup-ready corn and soybeans are a perfect example. Roundup is a glyphosate-based herbicide that, by definition, kills plants. In order to be able to spray it in large amounts without killing the crops it was meant to protect, researchers developed food crops that have a gene that makes them resistant to glyphosate. So, the corn and soybean crops survive herbicide treatment, while all the competing “weeds” are killed off.

All this means is that industrial farms are sprayed with more herbicides. And people are consuming those herbicides in larger and larger quantities. The results are likely to be extremely detrimental from both human and environmental health perspectives.

There has been a dramatic increase in the incidence of celiac disease in the last 50 or so years. The increase isn’t the result of improved diagnostic tools. In a study from 2009, researchers tested over blood samples taken from young adults between 1948 and 1954 and compared them to a matched sample of people living in the last 5-10 years. The rates of undiagnosed celiac disease were 4 times greater in blood samples from the recent group than in the samples from 1948-1954. This study is really important because it shows us that increased rates of celiac disease are very likely the result of something other than improved rates of diagnosis.

There is speculation that glyphosate (the active ingredient in Roundup) may deserve at least some of the blame. Glyphosate may interfere with breakdown of complex proteins in the human stomach, leaving larger fragments of wheat in the human gut that will then trigger an autoimmune response, leading to defects in the lining of the small intestine that are characteristic of celiac patients. In experiments, fish exposed to glyphosate develop both the digestive symptoms of celiac disease and the intestinal lining defects similar to those seen in celiac patients.

So, what does this have to do with the gut microbiome? Recent studies provide evidence that glyphosate negatively affects the human gut microbiome. Glyphosate is widely touted as a “safe” chemical, because the pathway it interferes with to kill plants doesn’t exist in humans. However, and this is critical, many bacteria do possess that metabolic pathway. So, even though most ingested Roundup might just pass through our bodies, it doesn’t do so without taking some toll along the way. Additionally, it appears that glyphosate preferentially kills the good bacteria in the guts of animals, while leaving more harmful microbes untouched.

Specific to celiac disease, the bacteria that are positively and negatively affected by glyphosate are overgrown or underrepresented respectively in association with celiac disease in humans. To clarify, the beneficial bacteria that can protect against celiac disease through their interaction with gluten are negatively impacted by glyphosate, thereby creating a potential mechanism for the development of celiac disease. Meaning that, when the bacteria are removed from the system, so are their associated enzymes that assist with the digestion of gluten, which may then increase the incidence of celiac disease.

On top of this, pathogenic bacteria, which seem to be largely spared by glyphosate exposure, have the potential to create another unique set of problems in the digestive tract. Pathogenic bacteria can trigger the secretion of zonulin, a protein which is known to promote intestinal permeability (leaky gut). Leaky gut is widely considered to be at least partially to blame for a slew of illnesses, including autoimmunity, heart and liver disease, and cancer.

I focused quite a bit on celiac disease in this post, largely because there is a great deal of direct evidence for an association between glyphosate and celiac. However, we know that gut dysbiosis can contribute to an enormous variety of ailments beyond celiac disease, from heart and liver disease to cancer. Likewise, a healthy microbiome promotes overall health, including improved immune function, better functioning organs, improved injury recovery, and resistance to dementia, among numerous other benefits. Knowingly disrupting such a vital and delicate system will be nothing but detrimental.

At a time when we are learning new things about the microbiome on a daily basis, it is imperative that we take the steps necessary to promote gut health and move away from behaviors and exposures that disrupt the intestinal microbiome. Especially when we have direct evidence for steps we can take to do so. At the very least, I think it is critical that consumers are able to make educated decisions about their health. If I had my way, pesticides and herbicides would not be used at all. But until that happens, I would really like to have as much information as possible at my disposal as I try to navigate what feels like an increasingly toxin-filled planet.



Asmar et al. (2002). Host-dependent zonulin secretion causes the impairment of the small intestine barrier function after bacterial exposure. Gastroenterology, 123(5), 1607-1615.

Fasano, A. (2011). Zonulin and its regulation of intestinal barrier function: The biological door to inflammation, autoimmunity, and cancer. Physiological Reviews, 91(1), 151-175.

Hershko, C. & Patz, J. Ironing out the mechanism of anemia in celiac disease. Haematologica, 93(12), 1761-1765.

Krüger, M., Shehata, A., Shrödi, W., & Rodloff, A. (2013). Glyphosate suppresses the antagonistic effect of Enterococcus spp. on Clostridium botulinum. Anaerobe, 20, 74-78.

Samsel, A. & Seneff, S. Glyphosate, pathways to modern diseases II: Celiac sprue and gluten intolerance. Interdisciplinary Toxicology, 6(4), 159-184.

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