How Soil Microbes and Intercellular Communication Affects Human Health

Story at-a-glance

  • There’s no such thing as “junk” DNA. As it turns out, this DNA plays an absolutely crucial role in regulating the 25,000 genes that actually make proteins
  • Thirty percent of our circulating micro-RNA, the switches that regulate protein production from our genes, are not from a human source — they’re from the bacteria and fungi obtained from your food and environment
  • When a plant is lacking in nutrients, it is attacked by pests. The same phenomenon occurs in your body — the loss of nutrients makes us vulnerable. This is why antibiotic use must be reduced in all its forms, in medicine, animal agriculture and GMO crop production with glyphosate-based weed killers


This is an older article that may not reflect Dr. Mercola’s current view on this topic. Use our search engine to find Dr. Mercola’s latest position on any health topic.

By Dr. Mercola

Your health is in large part determined by the health of the soil in which your food is grown. In this interview, Dr. Zach Bush delves into the many reasons why this is so.

Bush, who is triple board-certified in internal medicine, endocrinology and metabolism, and hospice and palliative care has done some fascinating and innovative research in this area and is one of the brightest physicians I have ever met.

He began his career as a conventional cancer researcher funded by the National Institutes of Health (NIH).

When his funding dried up following the 2008-2010 recession, Bush transitioned into nutrition, eventually coming to understand how chronic inflammation and loss of intercellular communication is at the core of all disease, and why so many of our foods have lost their medicinal value.

His science team's work has contributed to the new science of micro-RNA, the result of all that "junk" DNA in your body (accounting for more than 90 percent of the DNA sequences in your genome).

As it turns out, this "junk" DNA and the resulting micro-RNA play an absolutely crucial role in regulating the 25,000 genes that actually make the proteins that build your body. The micro-RNA function as "on/off" switches for the genes. Depending on the micro-RNA input, a single gene can code for any of more than 200 protein products.

What's more, 30 percent of the micro-RNA switches that regulate genes' production of proteins do not have a human source — they're from the bacteria and fungi obtained from your food and environment. Truly, this interview is one you will not want to miss! So, sit back, have a listen and prepare to be blown away.

The Road From Cancer Research to Nutrition

During his endocrinology and metabolism fellowship, Bush was managing diabetes, autoimmune disorders, metabolic disorders and infertility in his clinic; in his research role at the University of Virginia, he focused on cellular biology research, looking at novel mechanisms by which cancer cells can kill themselves.

It's a commonly held view that cancer involves a battle between your immune system and the cancer cells; however, Bush's research demonstrated the critical role of cancer-cell suicide in the body's management of cancer.

The redox (reduction and oxidation) communication molecules are the foundation of this important response system.

As long as there's sufficient cell-to-cell communication, the cancer cells should recognize that they're damaged beyond the point of repair and commit suicide, a process called apoptosis, or programmed cell death.

So why does that process fail in so many people? And beyond cancer, why are so many people struggling with so many chronic illnesses?

"We were seeing this explosion of type 2 diabetes, obesity, metabolic collapse, cardiovascular disease and, of course, cancer … It ended up being patients that [changed] my 17 years of intense academic training in cellular biology. I started thinking … there's got to be a better mechanism by which to [treat] this …

[In] clinic … I was using more and more pharmaceutical drugs to tackle [diabetes]. [But] it doesn't take long to realize there are huge downsides to the pharmaceutical approach. There are huge limitations to efficacy. There's enormous toxicity …

[P]atients were looking great on paper — blood sugars would come down — but they were getting worse clinically. More edema, more weight gain, more fatigue, more depression. Every ounce of insulin I put them on was more disease. It was this Catch-22 situation.

It was my patients that started to help me out of that box that was … starting to get me very depressed. It was really these root-cause questions my patients were asking that I felt incredibly unequipped to answer …

Ultimately, they had an intuitive knowledge that … food must have something to do with it. I kept sending them to the diabetes educators who would teach them a low-carb diet. It turns out that type 2 diabetes is not caused by carbohydrates."

Disease Is Loss of Cell-to-Cell Communication

Bush realized something was terribly wrong with the dietary recommendations his patients were receiving when they kept getting worse despite being fully compliant with the diet.

One of the first tip-offs that something was wrong with the patient education system was when he realized that hotdogs were listed as an acceptable staple diabetic food in the nutrition material they were receiving from the dieticians at the university.

"I had these patients that were eating, [for] breakfast, lunch and dinner, hotdogs with no buns," he says. "They thought they were now on a healthy diet because they were eating no carbs. This was the first red flag … That hotdogs are even on anybody's list of nutritious foods is somewhat dumbfounding.

That it could somehow be interpreted as the only food they should be eating was truly amazing. Those were some of the foundational cracks. But I felt profoundly unprepared to start to enter into that diet or nutrition conversation because I had no training in it …

Our [medical] education is so slanted away from lifestyle and … toward pharmaceutical management of chronic disease. Then, really, the blinders came off."

In a nutshell, Bush discovered that the process occurring in necrotic tissue, such as that of a diabetic ulcer, behaved almost identically to cancer cells viewed under a microscope.

"I said, 'My gosh. There's no such thing as diabetic ulcers. There's no such thing as cancer. There's no such thing as disease. There's only a loss of cell-cell communication,'" he says. "There's only a loss and isolation … that leads to this broken state … That was a huge transformational moment."

The truth Bush discovered can be likened to the analogy of light and dark — you cannot have both in the same place. If you shine a light in the darkness, darkness disappears. Health is like the light, and if you have health, you're just not going to be sick.

The Chemoprotective Intelligence in Soil

Bush left academia in 2010 to enter the world of nutrition. He opened a plant-based nutrition clinic to reach out to one of the poorest counties in Virginia, figuring if he could make a difference here, the same principles could be applied anywhere.

"I was just pounding my patients with the best nutrients I could find in the garden and helping them learn how to grow food. Frustratingly, there was a good 40, 50 percent of them that weren't responding in the right direction.

There was this amazing miracle happening to the 40 percent of them where conditions of decades were just melting away under the force of nutrition. But then there was this huge percentage that no matter how much nutrition we tried to bring to the plate, they were getting worse, not better."

He began questioning the science on nutrients' impact on mitochondrial metabolism. Then, a colleague named William Vitalis brought in a 90-page white paper on soil science, which led to another breakthrough in thinking.

"Around page 40, there's this big picture of a molecule sitting there that stopped me in my tracks … The blinders came down for a moment and I said, 'That looks a lot like the chemotherapy I used to be making. What is that doing in soil?' That was the moment we started turning our attention to the possibility that there was intelligence in the soil," Bush says.

One factor contributing to our rising cancer burden is the fact we've been using industrial farming practices for close to a century — practices that decimate the soil by disturbing and killing the microbes therein. We've essentially undermined public health from the roots up. If you don't have healthy soil, you can't grow healthy foods because the necessary micronutrients aren't there. As a result, even if you think you're eating some of the healthiest foods available, you're going to be deficient in micronutrients.

As noted by Bush, plant health correlates to and parallels human health. One of the very first things that happens when a plant is lacking in nutrients is that it will be attacked by pests. The same phenomenon occurs in your body. Conventional farming addresses this problem with chemical pesticides. In humans, we address it with antibiotics. However, both lead to resistance, and the more drug-resistant these microbes get, the worse the disease gets.

How Glyphosate Has Decimated the Medicinal Value of Food

In 1976, glyphosate was introduced. This is the active ingredient in a vast majority of weed killers on the market today, including Roundup®. However, this chemical does not selectively kill weeds. Any plant sprayed with this chemical will die — which is why Monsanto and other pesticide producers came up with the idea of creating herbicide-resistant plants through genetic engineering.

"It's worthwhile noting why it kills plants," Bush says. "Glyphosate blocks an enzyme pathway … called the shikimate pathway. These enzymes are responsible for making some of the most important compounds in food [including] ringed carbon structures, such as tryptophan, that are the backbone of hormones.

If you take away tryptophan from the plant chain or the plant kingdom by killing this pathway in bacteria and plants, the plant cannot make these essential signaling molecules … It wipes out about four to six of the essential amino acids, which are the building blocks for all proteins in your body … There are only 26 amino acids. You take away four to six of those [and] you just lost a huge percentage of biology.

But that's just the beginning of the problem that we're talking about in nutrition. This is, I really believe, the answer to why we were feeding all these healthy foods to our patients [yet] not seeing health benefits: There's a family of compounds called alkaloids … [When you] remove the alkaloids from food, what you see is the disease burst we have going on across so many organ systems in our bodies.

There's a family of [alkaloids] that are anti-parasitic … [others] are antidiabetic … anticancer … antihypertensive … anti-mood disorder … antiasthma, anti-eczema type of compounds. You go through the list of alkaloids and [realize that if you add a] chemical to our food chain that wipes out the production of [alkaloids] …

we [lose] the medicinal quality of food that has existed for thousands of years … [By using glyphosate] we robbed the soil and the plant from the ability to make these essential medicinal [compounds]."

According to Monsanto, glyphosate cannot affect human health because humans do not have the shikimate pathway. However, human gut bacteria do, as do soil bacteria and plants. Moreover, the human body cannot make its own alkaloids and essential amino acids. You must get these compounds from plant foods that feed off bacteria in the soil.

Glyphosate Is a Major Health Threat

Glyphosate also disrupts intercellular communication, which is at the heart of virtually all disease. To understand this, you first need to understand that bacteria, fungi and other microbes work in concert — there are relationships at play where certain ones help keep others in check. Unfortunately, since the discovery of penicillin we've essentially waged war against bacteria, with antibiotics often considered cure-alls by doctors and patients alike.

An estimated 7.7 million pounds of antibiotics are prescribed to Americans every year, equaling over 800 prescriptions for every 1,000 individuals. Since the 1960s, antibiotics have also been added to animal feed to promote faster weight gain. An estimated 300 milligrams of antibiotics are used for every kilogram (2.2 pounds) of beef produced, totaling nearly 30 million pounds per year.

In addition, farmers also use 5 billion pounds (over 2 billion kilograms) of glyphosate per year, worldwide, making glyphosate weed killers the most prevalent antibiotic on the planet.

In fact, that was part of the original glyphosate patent, stating its function to kill soil bacteria. So, antibiotics are used in medicine, meat production and on plant crops. By using glyphosate on our crops, neither the soil nor the plants can produce the medicinal alkaloids or any of the essential amino acids your body requires, and this appears to be a major part of why more than half of Americans are chronically ill.

"Glyphosate … is an organophosphate. [It is] called glyphosate because its backbone is glycine, which is one of the most essential amino acids that's extremely rich in your extracellular matrix … Your extracellular matrix, your neurons and many tissues rely on glycine as an amino acid building block. Glyphosate is glycine with a phosphate tagged on the end of it, and an amine, which is a carbon oxygen compound, on the other …

Organophosphate molecules are a toxin that tragically is water soluble. For a biochemist, this is … Dante's hell opening up … Because if you have a water-soluble toxin … it's now infiltrated every sector of the water cycle … 75 percent of the rainfall [is] contaminated with glyphosate …

As consumers, we are waking up to reality … We're eating organic food … Yet, if it rained on [that] crop, you've got glyphosate contamination. [The] whole ecosystem is contaminated with a chemical that is an antibiotic."

Based on environmental levels, typical glyphosate exposure through diet is thought to be anywhere from 1 part per million (ppm) up to 40 ppm, depending on the food or water source, with an average intake per human in the 5-50 mg of glyphosate per day. Testing has revealed that women's breast milk can contain 760 to 1,600 times the amount of glyphosate allowed in European water systems, even if the mother is trying to avoid glyphosate contamination.

This is a true testament to how pernicious this chemical has become. When you combine glyphosate-contaminated breast milk with the sterile C-section birth, which prevents the infant from being properly exposed to its mother's microbiome, you have a perfect recipe for health disaster.

How Glyphosate Promotes Whole-Body Toxicity

Bush's team discovered bacterial communication molecules in soil in 2012. As they began to study the effects of this communication network in the human gut environment, they realized glyphosate's toxicity is closely linked to the lack of bacteria. This discovery brought many pieces of the puzzle together. As explained by Bush, the toxic effects of glyphosate in the human environment are directly tied to damage to specific protein structures in the gut and other membranes in the body.

"This protein is called tight junctions. It has multiple constituents, multiple little proteins that make up these large Velcro-like proteins that hook together and attach one microscopic cell to the next cell. [Starting] at your sinuses and [going] all the way to the rectum, you have a vast amount of cells that make up a single cohesive carpet or membrane or shield from the outside world — ideally.

That membrane … is your frontline of defense … It is a single-cell layer thick … The "Velcro" is loosened appropriately by biology to allow big macromolecules to come in and then it tightens up right behind. That is managed by a little protein we make in our body called zonulin. Zonulin is produced appropriately by molecules that need to get through the membrane. It touches the membrane [and] the gut epithelium makes zonulin. The zonulin opens up the tight junction …

Zonulin is the critical modulator of this permeability of the gut membrane. If zonulin starts to get overproduced and you can't check its production, it … leads to damage in the gut epithelium … All the gates open and everything it was supposed to keep out [in the intestines] is let in [to the bloodstream].

It turns out that zonulin is triggered very potently by glyphosate. What a sad story. Monsanto and other companies have been telling us, 'It's safe. You eat it and you'll pee it out at the same rate.' [But] that's really bad news. Because [to eliminate glyphosate it has] to not cross just the gut membrane, it has to cross the membrane of the hepatocyte, the liver cells; go from one bloodstream to the other [and] all the blood vessels are tied together with tight junctions.

Now you go to the blood-brain barrier — tied together with tight junctions. When that starts to leak, your brain's exposed. Then you get to the kidney, the critical organ for detox … It starts leaking. You can no longer build gradients to pull toxin out of the body … [Your] body just became a sponge for toxins and you live in a toxic world. This is how we have [the] disease rates we do today."

To Reverse Disease Rates, We Must Eliminate Glyphosate

One of the diseases heavily influenced by this gut permeability is autism. If the current trajectory continues, somewhere between 2030 and 2045 — a mere 13 to 28 years from now — autism is projected to affect 1 in 3 children. At that point, it will be impossible to maintain human productivity in any given sector. Society as we know it will collapse.

"There is no time for us to wait for legislation," Bush says. "If we don't band together and hurry up to get this message out there — that we have to stop spraying glyphosate right now — we're doomed." On the other end of the age spectrum we have Alzheimer's disease claiming our seniors at ever-growing rates — and that's if they live long enough to not die from cancer first.

"In my clinic, I see this almost on a monthly basis now … sarcomas in the bones or chronic bone marrow cancers. All these things that used to happen in 70, 80 or 90-year-old people are now happening in 5-year-old children, 3-year-old children. Not to mention the brain tumor epidemic that we have going on in children," Bush says.

Today, 1 in 2 adults also struggle with mental health problems. In 1900, that ratio was 1 in 100. All of these disease statistics and more correlate with dramatic changes to our food, specifically the loss of nutrients and medicinal qualities of our foods.

"Now, let's paint this all back to an amazing story of communication," Bush says. "What we found in 2012 is a bacterial communication molecule. There's a lot of complex biochemistry, but I want to boil this down to a nutshell. The word "redox" means reduction and oxidation … [R]eduction is the donation of an electron to an environment. Oxidation is the tearing away or removal of an electron. The most common oxidation you're used to seeing ... is rust … It's starting to erode itself …

Osteoarthritis, that's the rusting of a joint. Cardiovascular disease [is] the rusting of the vascular tree … What we discovered in 2012 was a redox molecule potential in soil made by bacteria. This was earth-shattering because all my cancer research had been on mitochondria.

Mitochondria look a lot like bacteria, but they're about 1,000 times smaller. They live inside your cells … Your neurons can have 3,000 mitochondria in a single nerve. The average across the whole body is about 200 mitochondria per human cell …

When mitochondria digest your food, they make balanced signaling of redox molecules. It's those redox molecules I was studying [when I said], 'Wow. We can use this communication network to empower a cancer cell to induce apoptosis' … Mitochondria rule the cancer cell if they make enough redox molecules. If they can get high enough oxidative stress in there, the cell will kill itself.

Fast-forward to 2012. What is that molecule in soil? Why is there redox potential in the soil? And then of course, bacteria don't have mitochondria. Only multicellular organisms … have mitochondria because we can't break down nutrients from the food by ourselves. We need the mitochondria to do that … Bacteria don't have mitochondria; therefore, they don't have all that redox signaling.

How do they balance an ecosystem of 40,000 species if they can't talk? The blow-my-mind moment of 2012 was, 'They are talking.' The bacteria are in communication. They know what balance looks like. They know how to change the system. To our shock, amazement and joy — I'm so glad to tell you this is all going to end on a good note, or at least an opportunity for us as humans to heal — … our bacterial communication network … [is] the antidote to glyphosate …"

Introducing a New View of Biology Where 'Junk' DNA Hold the Key to Health

For the first time, Bush and his team were studying human biology in the context of a fluid, fluent, robust bacterial communication system. They had never seen human cells in that environment under a microscope before, and it changed everything they believed about apoptosis, protein synthesis, genomics and more. As noted by Bush, "We never took into account the possibility that an ecosystem of fungi and bacteria could be dictating human cellular behavior in health."

Scientists have already concluded that environment is king when it comes to genetic expression. A single gene is now recognized to be able to make 200 different proteins depending on its environment. This was a total paradigm shift and really bad news for those banking on personalized medicine in the 90s, because this meant the genome is a warehouse of options waiting to respond to the environment; the human genes themselves are not determining the outcome of the biology.

If you calculate the possibility of one gene creating 200 outcomes and multiply that by 25,000 genes that code for proteins, there are many millions of potential health outcomes for your body — all based on the environment you provide. Now, the next generation of epigenetics is micro-RNA.

"In a classic move in science, we, as scientists, took a look at the genome and said, 'We only have 25,000 genes … that code for 200,000 proteins … We're only a little less than twice as complicated as the fruit fly when it comes to genes … But the stunning reality is that 90 percent of the DNA doesn't code for a gene that's going to code for protein — over 90 percent!

We just called that junk DNA … Well, in the last five years, it's become obvious that the junk DNA is doing something. Not surprisingly, it's the junk DNA that's actually regulating the 25,000 genes that actually make protein[s]. How does it do that? Each little strip of junk DNA makes a micro-RNA that's never going to code for protein. Instead, the micro-RNA functions as a switch. It now goes into the bloodstream and into other cells to turn on and off gene behavior.

The stunning reality of your ecosystem and human health is that 15 percent of the on and off switches in your bloodstream are not from you. They're from the bacteria in your gut and the bacteria you breathe. Another 15 percent are from the fungi in your environment. Thirty percent of the on and off switches that are determining what gene is going to code for what protein … [have] no human source …

What does this mean for us as humans? We have got to get back in touch with our ecosystem. We have got to get a complicated ecosystem back. We have got to stop taking antibiotics, for sure. We need to stop eating and spraying antibiotics all over our food and soil.

We have to stop disrespecting this normal balance of ecosystem. We need to start getting back outside … We have to make our workspaces look different. We have to really get people back out and inject ecosystem back into their day-to-day lives."

More Information

Bush has authored a book titled "Gut Biome," which is expected to be published this summer. If this interview has whet your appetite for more, do keep your eyes peeled for the release of that book. What we covered here is a mere fraction of the information Bush and his team have uncovered.

While the scope of the problems we face are beyond what most of us can even imagine, with this new understanding new solutions become apparent and, with that, new hope.

"What we see in the clinic is that as soon as you put this bacteria [in] communication, we're back into play," Bush says. "We outsourced our food. We outsourced our nutrition … I think we are responsible, each of us in a small way, for what Monsanto and the chemical companies became, because we stopped doing it ourselves.

We need to take back that control. How much power is that? We should be super empowered as consumers to say, 'With a little bit of collaboration, with a little bit of discussion, we can change everything.' That's what we'll do."


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