Our Food System & The Rise of Superbugs and Drug-Resistant Fungi

Our Food System & The Rise of Superbugs and Drug-Resistant Fungi

Vivian Kanchian
Vivian Kanchian
March 22, 2023
9 min

Have you ever stopped to wonder where your food comes from? What resources (water, fertilizer, human and mechanical labor) went into producing it? How did this affect the environment and the people working on the land? Was the soil left healthy after harvest? And perhaps the most important question of all: why does it even matter?

It matters because if you eat, you may be interested to know that the industrial food system is at the root of most of our current-day issues. How we produce food influences not only what we eat but affects everything from water, food, and national security, to biodiversity loss, climate change, and public health – because everything is connected.

You might have heard that pharmaceutical companies are starting to produce more vaccines. Currently, the US government is considering vaccinating all chickens in the country against a potential bird flu outbreak. Additionally, the USDA has approved a honeybee vaccine to prevent bacterial disease, and researchers are exploring the development of a vaccine for drug-resistant fungal infections in humans. Drug resistance occurs when infections no longer respond to available medications, which is highly concerning. Folks, this ain’t normal.

Industrial farming and the rise in superbugs

For a long time now, wildlife experts have sounded the alarm about the risks of factory farming. Aside from being inhumane, the way we crowd chickens into small spaces breeds disease and makes it possible for dangerous mutations to occur in once-benign fungal pathogens. Until 2017, broad-spectrum antimicrobial drugs were abundant in industrial farm animals. In a disingenuous attempt to curb the growing spread of medication-resistant infections, the FDA has since restricted them to veterinary-approved use for animal disease prevention, treatment, and control. But since the petri dish conditions of factory farms have remained the same, they are still being used often to treat infectious diseases. Industrial agriculture (a kissing cousin of the pharmaceutical industry) continues to perpetuate the myth that because most of the antimicrobials used in animals are not used on humans, they don’t pose a threat to public health. The truth is, epidemiologists are aware that their repeated use creates superbugs that have figured out how to defy multiple medications.

As for the precious honeybees, historically, a typical hive or colony in the US declines by about five percent during a good year, and up to twenty percent in a bad year. Over the last decade, beekeepers have seen a 30-50% population decline every winter. This is terrible news considering bees are responsible for a third of the food we eat. The good news is that scientists know various interrelated reasons for this occurrence. Among those factors are antimicrobial pesticides, drought, habitat destruction, malnutrition, air pollution, and climate change. All, of course, are connected to the way we produce our food.

In 2019, the Centers for Disease Control and Prevention (CDC) identified three drug-resistant fungi that they believe pose varying levels of concern to human health: Candida auris was labeled an “urgent threat,” while drug-resistant strains of Candida are viewed as “serious threats,” and azole-resistant (aka fluconazole) Aspergillus fumigatus is now on a “watch list.”

Infectious disease researchers think that antifungal resistance arises from a few sources: 

  • A growing number of immunocompromised patients are treated with these drugs.
  • The prevalence of fungicide use in agriculture. 
  • Certain fungi are inherently resistant to some classes of antifungal drugs currently available. So, when they morph to dodge even a couple of these, treatment options can become limited.

Fungi & humans – an intertwined evolution

It is important to note that humans, and the planet we inhabit, with all of its various life forms, have evolved alongside fungi for over a billion years. As a matter of fact, we share almost fifty percent of our DNA with fungi. Out of the 150,000+ mushrooms that have been identified, only about 200 of them are deadly to humans. Sure, they can sometimes harm us. But ultimately, we are longtime allies. Given this rich history we share, could we take a moment to entertain the idea that a root-cause approach to superbugs may save us a lot of lives and money in the long run? Is it possible that the solution lies in working with nature and not against it? After all, it has been doing its thing for much longer than modern science. We unravel an intricately entangled web of life whenever we mess with nature’s complex symbiotic relationships. Doing so makes things much more complicated for ourselves than necessary. 

A perfect example of this is the conundrum that doctors and scientists now face with the rising occurrence of antimicrobial resistance. According to the CDC, invasive fungal infections that develop the ability to break through the skin and enter the bloodstream pose the biggest concern.

Researchers believe cells become resistant to antifungal drugs in two ways:

  1. Non-genetically; these types of cells are still responsive to antifungal drugs.
  2. Genetically; these types of cells have undergone mutations – making them permanently resistant to certain antifungal drugs.

There is a space between these two phases, with a mix of different types of drug-resistant cells that scientists are currently exploring. The hope is that once they understand how certain cells become permanently resistant while others do not, doctors can offer strategic treatment plans for patients. This could include using alternating drugs to zero in on cells still receptive to medication. Researchers are banking on the idea that this approach may delay the permanently drug-resistant cells from taking over. Another possible strategy would target the chitin in the cell walls of fungal pathogens. Chitin is a substance crucial to fungi’s survival, helping both physically and chemically protect them from foreign invaders. 

Agriculture: problem and solution

Immune dysfunctions of all stripes have been strongly linked to the consumption of processed foods. Currently, seventy-three percent of the American food supply consists of ultra-processed foods. Surely, an overhaul of our food system could have widespread health benefits. 

Take, for example, the two most commonly diagnosed diseases in American men and women – breast cancer and prostate cancer. Both have been linked to a deficiency in manganese – an essential trace mineral we get from food  (1),(2). In addition, ninety-five percent of the food we eat comes from soil heavily treated with synthetic fertilizers, which are deficient in many nutrients and probiotics that help build the immune system (3). In a landmark 2004 study that tracked the nutrient content in 43 different fruits and vegetables, scientists found “reliable declines” in protein, calcium, phosphorus, iron, vitamin B2, and vitamin C (4). More recently, the Bionutrient Institute tested a variety of crops from different soil to see how their nutrient content would compare — apples to apples. Their study on blueberries revealed that you would need to eat eight times the amount of blueberries grown in degraded soil compared to the same fruit grown in nutrient-rich soil! 

Moreover, America’s use of systemic pesticides like glyphosate (aka Roundup) cannot be washed off before consumption. The use of glyphosate has skyrocketed over the last thirty years, and the most common crops it is used on are corn, soy, and wheat – the same ingredients that are consistently found in processed foods. So, in addition to eating nutrient-deficient junk foods, we are ingesting a toxic chemical that has been shown to increase the risk of cancer diagnosis by forty-one percent (5). Many of these crops are also grown to feed farm animals, and studies show they kill the beneficial bacteria called bifidobacterium in chickens’ guts. Are you beginning to see how these practices might be connected with a widespread chicken virus?

Sir Isaac Newton once famously said that “every action has an equal and opposite reaction.” For instance, cancer cells become emboldened in response to chemotherapy  – fighting even harder for their own survival (6). Doctors use the word remission when a patient’s cancer retreats because they know those cells can mutate in response to treatment later on. Given this rule of thumb, what is the likelihood that we will outsmart nature for very long by inventing a fungus vaccine?

The complex problems we face call for an equally complex solution that can only be found by returning to nature. Just imagine the butterfly effect on overall public health if we change how we grow food. We wouldn’t need to treat so many living beings with antimicrobials because they wouldn’t be so immunocompromised in the first place. And perhaps, we wouldn’t need to venture down the slippery slope of vaccinating everything in sight.

Transforming our food system to more regenerative practices is one of the most holistically impactful actions we can take toward building a more resilient future.

Indigenous communities have practiced regenerative agriculture for centuries. It goes beyond sustainability – helping to build soil and biodiversity and leaving the land better off than we found it. The practice operates on these general principles:

  • Soil armor. Keeping the soil covered with crops between harvests acts like a sponge – holding water and nutrients in when it’s windy, rainy, and during times of drought.
  • Living roots. Keeping the roots of plants in the soil, instead of pulling them out between harvests, keeps beneficial microorganisms and nutrients in. It also helps soil stick together, making it more resilient to disruptive weather events. Mycorrhizal fungi play an essential role here, attaching themselves to the roots of plants to help them soak in more water and nutrients from the soil.
  • Diversity. A variety of microorganisms, plants, and animals on the farm creates healthy soil, hardy crops, and resilient natural systems that don’t need chemicals to manage pests and diseases. Everything is there for a reason — to create overall balance.
  • Livestock integration. Among their many benefits, ruminant animals like cows, sheep, and goats improve soil health (without added chemicals) and increase biodiversity.
  • Minimizing soil disturbance. Tillage is the process of turning over and breaking up soil. Reducing or eliminating tilling protects the microbes and nutrients that make their home there.

To learn more about how regenerative agriculture (aka biodynamics) supports life, check out this short video.

The soil-gut connection

Some of the world’s most ancient medicine philosophies, like Ayurveda and Traditional Chinese Medicine (TCM), have emphasized the importance of gut health for human well-being. More recently, scientific evidence has affirmed that many infections in immunocompromised people begin with an unbalanced gut microbiome. A nutrient-poor, chemical-rich diet combined with treatments like antimicrobial and chemotherapy drugs can wreak havoc on a healthy immune system. As a result, the intestinal lining, which is responsible for keeping good bacteria in and bad bacteria out, can be weakened and less effective. Because seventy percent of our immune system lives in the gut, this can open us up to systemic infection (7). 

Not too long ago, humans lived in rural settings, exposed to a variety of microbes from soil, animals, and even feces. These conditions are how we built our immune system. Now, we over-sanitize, take antibiotics, and eat a low-fiber diet of processed foods that exacerbate our loss of beneficial microbes. Add to that the loss of soil biodiversity in many areas, and we create the perfect conditions in which destructive pathogens love to thrive.

Curiously, a plant root behaves much like our lower intestine and contains around the same amount of microorganisms (8). The only difference is that plants acquire nutrients from the outside and humans from the inside. Because plants can’t absorb minerals on their own, they use soil as their stomach. The microbes and fungi that live there break up and digest bits of bedrock into nutritious minerals. In return, plants leak out a sticky substance from their roots called exudate that nourishes both soil and the microbes that live there. When antimicrobial fertilizers and chemicals weaken soil, it becomes more susceptible to external factors like wind, drought, and floods washing away its protective surface layer. Also, the lack of nutrients and good microbes leaves soil (and the plants that grow in it) malnourished and more vulnerable to disease.

In simple terms: healthy soil = healthy plants = healthy humans.

To sum up, the choice is ours. We can continue to fight nature every step of the way as we face an ever-increasing number of superbugs. Or we can take a good hard look at our food system and ask ourselves: “How’s that working for you”?

“Food Fight” author Daniel Imhoff calls the US Farm Bill “the most important legislation that most citizens [have] never heard of – and one that [affects] them three meals a day.” The Farm Bill affects everyone who cares about local food systems, health care, school food, climate change – or anyone who happens to pay taxes. This piece of legislation is typically renewed every five years and is up for renewal in October 2023. 

To learn more about how Regenerate America is working to transform our food systems into more regenerative practices and to take action by signing the petition, please click here.


  1. Shen, Fei, Wen-Song Cai, Jiang-Lin Li, Zhe Feng, Jie Cao, and Bo Xu. 2015. “The Association between Deficient Manganese Levels and Breast Cancer: A Meta-Analysis.” International Journal of Clinical and Experimental Medicine 8 (3): 3671–80. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443096/#:~:text=Some%20clinical%20studies%20find%20that.
  2. Saleh, Saleh A.K., Heba M. Adly, Altaf A. Abdelkhaliq, and Anmar M. Nassir. 2020. “Serum Levels of Selenium, Zinc, Copper, Manganese, and Iron in Prostate Cancer Patients.” Current Urology 14 (1): 44–49. https://doi.org/10.1159/000499261.
  3. Bagnall, Dianna K., John F. Shanahan, Archie Flanders, Cristine L.S. Morgan, and C. Wayne Honeycutt. 2021. “Soil Health Considerations for Global Food Security.” Agronomy Journal 113 (6): 4581–89. https://doi.org/10.1002/agj2.20783.
  4. Davis, Donald R., Melvin D. Epp, and Hugh D. Riordan. 2004. “Changes in USDA Food Composition Data for 43 Garden Crops, 1950 to 1999.” Journal of the American College of Nutrition 23 (6): 669–82. https://doi.org/10.1080/07315724.2004.10719409.
  5. Zhang, Luoping, Iemaan Rana, Rachel M. Shaffer, Emanuela Taioli, and Lianne Sheppard. 2019. “Exposure to Glyphosate-Based Herbicides and Risk for Non-Hodgkin Lymphoma: A Meta-Analysis and Supporting Evidence.” Mutation Research/Reviews in Mutation Research 781 (February). https://doi.org/10.1016/j.mrrev.2019.02.001.
  6. S. Arbab, Ali, and Meenu Jain. 2016. “Cancer Therapeutics Following Newton’s Third Law.” Biochemistry & Physiology: Open Access 01 (05). https://doi.org/10.4172/2168-9652.1000e145.
  7. Taur, Ying, and Eric G. Pamer. 2013. “The Intestinal Microbiota and Susceptibility to Infection in Immunocompromised Patients.” Current Opinion in Infectious Diseases 26 (4): 332–37. https://doi.org/10.1097/qco.0b013e3283630dd3.
  8. Blum, Winfried E.H., Sophie Zechmeister-Boltenstern, and Katharina M. Keiblinger. 2019. “Does Soil Contribute to the Human Gut Microbiome?” Microorganisms 7 (9): 287. https://doi.org/10.3390/microorganisms7090287.

Fact Checked: Seraiah Alexander


Vivian Kanchian

Vivian Kanchian

Content Writer

Table Of Contents

Industrial farming and the rise in superbugs
Fungi & humans – an intertwined evolution
Agriculture: problem and solution
The soil-gut connection

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