Connecting Large & Microscopic Environments

Dr. Zach Hil

What follows is an interview with Dr. Zach Bush, a physician and internationally recognized educator working at the intersection of the microbiome, human health and disease, and our food production systems. We asked for his insight into the root causes of today’s gut health concerns, and his responses indicate the need for major changes in the sectors of corporate agriculture, Big Pharma, and Western medicine. Dr. Bush’s research and businesses suggest a future based in regenerative health for the planet, and the humans who live here, is possible.

Fermentation: Conditions such as irritable bowel syndrome (IBS), small intestinal bacterial overgrowth (SIBO), and leaky gut seem to be the maladies of the moment. They also seem to be a stopping point in conversation or diagnosis for the allopathic community, but a starting point in conversation for naturopathic and integrative medical communities. Why is this?

Zach Bush: I don’t know that I have the entire answer, but the underpinnings of it, I believe, come down to the segmented nature of education at the allopathic level. You have gastroenterologists, cardiologists, pulmonologists, oncologists, rheumatologists; all of these areas of expertise are trained away from understanding the whole picture of health. None of the conditions you described fall into the above specialties. There’s never been a microbiome specialty to coordinate the education or expertise in this area of medicine; even our lauded federal agencies of the NIH (National Institutes of Health) and FDA (Food and Drug Administration) don’t yet recognize the microbiome as a source of disorder or disease at this point. The traditional segmentation of an allopathic medical education has failed to find a home for microbiome expertise.

You would guess the gastroenterologist to be an obvious champion in this field, yet we find this subspecialty often the most resistant to this information. I think this has to do with education. They’re really trained as optical technicians, spending much of their time looking through scopes at the colon, at the stomach, at the small intestine via cameras, and so they have a very gross anatomical look at the body.  They’re not molecular biologists by and large, and learning isn’t cross-pollinated with gastroenterology, for example. When you learn gastroenterology without studying the microbiome (which seems hard to believe for the consumer at this point), you’re taught to believe the GI tract is a simple anatomical tube, and not a complex ecosystem that maintains optimal metabolism, immunity, and nutrient delivery via an intricate matrix of epithelial barrier cells, endocrine cells, nerves, immune cells, and beyond.  This educational limitation not only excludes the microbiome, but also the more intricate reality of the microscopic function of the gut lining. As such, there’s been huge pushback, even categorical denial, from allopathic gastroenterology about pathologic gut permeability or “leaky gut” as a disorder that’s emerged as an epidemic underlying the chronic disease explosion in recent decades.

The technology-driven specialties can maximize billing through imaging technology: Radiology, interventional radiology, interventional cardiology, and gastroenterology are the last bastion of economic profitability in hospital systems.  The industry rewards practitioners in these fields with the highest salaries in the physician world.  If gastroenterologists make their money understanding the GI tract as a tube, there’s no incentive to study or to teach nutrition, microbiome, or microbiologic physiology as a focus for clinical training. Interestingly, despite global recognition over a few thousand years that food is our medicine (tracking back to ancient Chinese medicine teachings and Hippocrates of ancient Greece), nutrition has been completely left out of medical education at large, which is where we meet the microbiome at the largest level, through food and the water systems that populate our guts. Education is the short answer to why it is that allopathic medicine is so far behind the science that even the general consumer has come to understand.

Fermentation: Along with a rise in gut maladies is another trend:  fermentation. Fermented products are increasingly popular remedies and restoratives for current gut maladies. Can you discuss this, especially within the context of the data you’ve collected?

ZB: To better understand the relationship between ferments and the human microbiome, we first need to understand the relationship between the gut and the greater environment in which we live. This emerging field is best encapsulated through research led by Jeff Leach, founder of the Human Food Project and co-founder of the American Gut project. His research, published in Science in 2018, studies the gut microbiome of some of the last hunter-gatherer tribes in Tanzania, their original and diverse gut microbial populations and their relationship to the greater microbiology of the African environment. Not surprisingly, the tribes’ nonindustrial lifestyle results in a more traditional human microbiome with vastly more diverse bowel environments than the typical American consumer; their diversity is 10 times greater, if not more. Leach’s work has demonstrated that a human gut microbiome, when integrated with nature through outdoor habitation and daily outdoor activity, is an immediate extension of the greater ecosystem in which the person lives. 

Additional research in the journal Cell demonstrates similar effects of antibiotics in lab rodents and humans in their daily Westernized environment.  The antibiotic, taken over a two-week period, eliminates about 80 percent of the biodiversity in the gut. As such, if you take an antibiotic as an American, you do a huge damage to your gut microbiome. In contrast, a missionary group delivered antibiotics to the hunter-gatherer group, saying, “If you ever get sick, you can take these.” The tribe, however, didn’t really have an understanding of the word “sick.” The concept of infection was foreign to them. So, the tribe sat around the fire that night talking, and instead of waiting to learn what “sick” was, they ate all the shiny antibiotic capsules that night. The study group was terrified that they’d just lost the last living examples of intact, nonindustrial human microbiomes on the planet, but continued to do their required daily collection of stool samples, which were sent to U.S. labs for genomic analysis. It was with shock and awe a month later that they examined the data and found that the antibiotics had a minimal effect on the biodiversity in the guts of these tribal people. What it demonstrates is that these people are so in touch, at every point in their day, with their greater macro-ecosystem, that their guts are just a small extension of the vast biodiversity around them, and you really can’t do damage to the limited space of the human gut as long as humans stay in touch with their macro-ecosystem. So it’s a lesson to us as consumers; it’s our isolation from the macrobiome and nature at large that makes our gut ecosystem so vulnerable to injury.

This is where fermented foods enter the conversation. The fermentation process is an amazing tool that brings the vast marco-ecosystems of the natural world back into the environments of our gut.

Fermented (preserved) foods have been in the human diet for many thousands of years, but experience tells us these foods are medicinal with a specific impact on gut health and metabolism. If you lead a meal with a tablespoon or so of fermented food, it improves digestion, reduces instances of inflammation, acid reflux, and all sorts of other conditions. The combination of those medicinal properties and the data that’s coming out of Leach’s open-source American Gut project help us recognize our food system as an important entry point for reconnection with the macrobiome. When you ferment, a complex system of bacteria and fungi start to process the food item; microbes slowly reduced the food into metabolites and breakdown products that intelligently convert, transform, and deliver nutrients and medicines from fermentation to you by that microbiome digestive process.

A word of caution about the fermented food industry: The majority of products on the market are fermented through a probiotic-like effect. They’re not made by wild fermentation. Most commercial yogurts, kefirs, and fermented beverages on the market are made using a technique in which very few strains of Lactobacillus species, including L.acidophilus, for example, are replicated by the billions and added to foods to ferment them. While these foods provide some probiotic benefit to consumers, they’re limited by the select species of microbiota replicated as opposed to the diversity that’s possible with wild fermentation. Mass fermentation takes a couple of strains of Lactobacillus spp., for example, and adds these to your food to ferment it. This is like taking a probiotic capsule or liquid preparation in which there are billions of copies of just three species or seven species in each dose. In this same way, fermented foods and probiotics have become a massive industry that completely misses the primary point of the last 20 years of microbiome science, namely, diversity is the entire secret to microbiological health. These kinds of probiotic-like products are currently valued at $30 billion worldwide. Unfortunately, the quickly accumulating science shows that we’re doing damage to the human microbiome through the use of these probiotic-like foods and supplements.

The peer-reviewed journal Cell published two articles in September 2018 that demonstrate probiotics have a powerful suppressive effect on the diversification of the microbiome following antibiotic exposure. In rodent and human studies, two weeks of antibiotics were given to each, resulting in an 80 percent loss of the gut microbiome. When a mouse was given back a fecal transplant with original stool material collected before antibiotic exposure, it had a whole microbiome again within 10 to 20 days. However, if the mice were given a commercially prepared probiotic, they didn’t recover their microbiome for the 50 day duration of the study.  The biome stayed just as suppressed on the probiotic as on the antibiotic. That’s devastating news to a world that puts SIBO and IBS patients on chronic probiotics, and nearly everyone prescribed antibiotics is given a probiotic after, which is now understood as possibly the worst time to take that probiotic. It’s clear that we’re slowing, not speeding, recovery.

Fermentation: So what would you recommend as an alternative recovery method?

ZB: One of the alternatives is to do nothing. In that same study, they had a placebo group. After the two weeks of antibiotics, this group returned to their normal lifestyles without any probiotics, and there was a complete recovery of their microbiomes within 30 days. So we’ve been sold a marketing campaign around commercially prepared probiotics, when the ideal of what they’re selling happens naturally through reconnection to your environment. You should get back to your outdoor life, your healthy nutritional environment, and all the rest.

The other alternative to commercially prepared probiotics is wild fermentation, which I’m a huge fan of. In a wild fermentation, you’re taking whatever it is you’re going to ferment and exposing it to the air itself, and to thousands of species of bacteria, fungal spores, and the like, available to create a diverse ecosystem within that food. This biodiversity can increase the nutrients available in the fermented food. Not only does the diversity of the microbiota increase, but there also develops an intricate communication network between various bacteria, fungi, and other microbes.

The final piece of the puzzle is to understand the breakdown products of fermentation— the metabolites made by the bacteria and fungi as they digest or ferment food — whether in your gut, in the soil, or in a product. And what we’ve found is that there’s a communication network produced by bacteria and fungi. We’ve become industry leaders in understanding the relationship of these communications molecules in systems of soil health, agricultural meat production in cows and poultry, all the way down to your companion pets that are having leaky gut, and of course, humans. What we’re learning is that, instead of adding bacteria and fungi in an effort to micromanage the gut microbiome, the sterile soil extracts of these carbon-based reactive molecules provide the communication network from those diverse ecosystems of bacteria and fungi to coordinate the communication between the microbiome elements, the gut and vascular lining, immune system, and even the mitochondria with the human cells. The science has developed products to aid in the recovery from the chronic antibiotic and herbicide exposure challenging humans, animals, and soil health every day. With these products, we see a very rapid recovery of the biomass of the stool and can demonstrate support to cell communication and intracellular repair pathways in gut and vascular cells.

Fermentation: What exactly is getting “extracted”?

ZB: There are tens of millions of small carbon molecules that we’ve come to call “carbon snowflakes” because, like a snowflake population that exhibits different crystal shapes in each snowflake, these carbon molecules vary in their intricate configurations depending on which species of bacteria and fungi have produced each one.

We’re extracting carbon metabolites, which, in a liquid state, allow for interaction of hydrogen and oxygen bonds on these carbon snowflakes and function as the wireless communication between the cells. We can picture this like a wireless network for your cellphone. Your cellphone has a transmitter and receiver that works all the time. If you’re more than 7 miles from the closest tower, you lose signal and you can no longer communicate with the world around you. The software begins to decay and fragment, you can’t update anything, and you become isolated; this is exactly what happens at the cellular level.

We’re starting to understand that the microbiome provides a networked system of communication between human cells that keeps the communication of repair and regeneration in flow. A human cell with unfettered access to information is always in a state of healing and repair.

In the event that it’s so damaged that it can’t repair, it replaces itself.  It goes through a self-suicide and calls in through the network for a stem cell to replace it. We never really understood how the symphony of health and healing worked. We never studied this in allopathic medicine. We study disease. When I left the university, I set out to start to understand the physiology of health and healing microscopically. This led me to the discovery of the communication network between the microbiome and human cells.  That’s what we’ve come to be in humble awe of; the microbiome is coordinating biology on earth, at the human level, at the earthworm level, and right on down the chain.

A map showing cancer death rates from 2012 to 2016 by state.

Fermentation: As the environment has shifted, particularly in the past 10 to 20 years, there have been rapid changes in the biodiversity of ecosystems. How has the diminished food and diversity we have access to affected our ability to support our microbiomes?

ZB: While we now understand that antibiotic usage in humans is detrimental to our microbiomes, and we look toward the environment, we’re learning that the animals and plants we eat are also at risk of diminished microbial diversity. When we eat animal proteins and plants, we increase our antibiotic exposure; we get five times the antibiotic exposure in our food chain than we do even in our doctor’s office. The exposure from prescribed medicine is dwarfed by the antibiotics we pour on our crops and into our soil. Roundup is the most famous example. Roundup has been patented as an antibiotic and beyond, meaning it kills the microbiome of the soil. As we decimate the microbiome of the soil, we decimate the fungi, mycorrhizae, bacteria — this complex infrastructure, this cityscape within the soil — and we end up with dirt instead. Soil is a living organism. Dirt is dead minerals in a nonorganic and nonbioavailable state.

By current estimate, we’ve depleted or killed about 97 percent of the agricultural soil on Earth, most rapidly in the last 30 years. In the U.S., we’re losing about 4,000 pounds of dirt per acre due to erosion and current cultivation methods, which equates to about 11 percent of our possible gross domestic product (GDP) being flushed down our water systems, into our rivers, and out to our oceans. This massive amount of topsoil needed for healthy food production is irreplaceable under current farming mechanisms, because as farmers we don’t understand how to build soil. The importance of this is becoming clearer when it comes to the impact on human health. If you look at the disease prevalence and Roundup spray maps in our country (see maps above and on Page 81), they line up perfectly over our soil depletion maps, suggesting that as we kill the microbiome, human death increases from cancer, neurologic degeneration, neurologic dysfunction, immune dysfunction, and metabolic collapse. It’s kind of the opposite story of what was discovered with the hunter-gatherer tribes taking antibiotics. Our health is a reflection of the greater ecosystem; many countries using Roundup’s antibiotic product, glyphosate, kill the microbiome and lose that greater reinforcement system for our gut biodiversity, that data bank of microbial intelligence that we should be adopting each day as we touch nature and eat food. Right now, China is the biggest producer and consumer of glyphosate.

The map on the left reveals river basins of the U.S. by Strahler Stream Order classification, thick lines representing higher order. The large pink area is a critical water source. Notice how this catchment runs through the middle of the country combining flows from the Continental Divide (west) and Appalachian (east) Mountain ranges into the Gulf of Mexico. Flow also moves from north to south. This catchment creates the fertile land used to grow food in the U.S. This U.S. Geological Survey map (center map) shows estimated agricultural use of glyphosate as of 2011. The dark-brown areas indicate use of more than 88.06 pounds of glyphosate per square mile of land. Glyphosate, which is a patented antibiotic used as a pesticide, is most densely used in the middle of the country, center of U.S. agriculture, and within the largest water catchment in the U.S. as noted in the map above. This National Cancer Institute map (right) reveals annual cancer deaths per 100,000 people, per state. Data are age-adjusted for all cancer sites, all races, and sexes. Red indicates that approximately 177.1 to 197.9 deaths per 100,000 in that state were caused by cancer, while dark-blue notes 116.1 to 151.0 deaths. Taken together, the same location in each map shows a direct correlation between fertile agricultural areas, heavy glyphosate usage, and high mortality from cancer.

Fermentation: Can you unpack “microbial intelligence” a bit? What does it mean for us to lose microbial intelligence? It sounds similar to quorum sensing.

ZB: Quorum sensing is typically within a single species. A simple demonstration is the rapid division and rapid replication of bacteria in a petri dish. As soon as the outer rim of those bacteria starts to bump into the walls of the petri dish, a signal is sent out that suddenly stops proliferation, and you get homeostasis of the population. Resources seem to be shared to ensure optimal use and abundance across the population. That’s quorum sensing.  The bacteria are somehow communicating amongst each other; what their population behavior should look like in regard to replication and reproduction, resource management, etc.  You can see this in multi-species situations as well, even in the macro-ecosystem of trees.

For example, on the African savanna, a giraffe might be grazing on big trees that encircle a grove. Within a few minutes, the trees sense that if they allow the giraffes to keep grazing, they’re going to be completely damaged and won’t have enough photosynthesis to stay alive, so they start producing acid in their leaves. The acid turns the giraffe’s attention to another tree. We’ve discovered that it’s not only the tree being eaten that’ll shift its acid production. Through quorum sensing, all the young trees in the grove will simultaneously be signaled to make acid so they’re the least likely to be eaten, and therefore will have the most advantage to continue to grow and replace the dying canopy of the older trees. So there’s a multigenerational coordination happening between the trees to maintain homeostasis with the giraffes.

Now, imagine quorum sensing not being just bacteria or trees, but 5 million species of fungi asking, “What do we need over here?” or “What type of fungi do we have over here?” Humans are only one species, and yet look at the difficulty we have communicating amongst ourselves. We have an imperfect concept of sharing, of a synergistic or co-creative lifestyle. We’re simply consumptive. But what we have in microbial intelligence is an intelligence that reflects the bounds of the universe, where matter itself takes on varied and different forms, yet knows intrinsically what balance should look like, and recognizes the special and integral role of every species. Shared microbial intelligence understands that the whole system fails with the loss of biodiversity. Microbial intelligence, I believe, isn’t only important for human health, it’s the only solution for social-political stability on the planet.

Fermentation: What can we do to promote microbial intelligence?

ZB: I encourage people to support Farmer’s Footprint (www.FarmersFootprint.us), which is a consumer-to-farmer coalition established to create a fair economy around real food production and a reeducation of the farming industry toward regenerative agriculture. The coalition teaches farmers how to become soil builders using regenerative techniques. We’ve seen dirt that’s been dead for 10 to 20 years under the pressure of Roundup (glyphosate) and other chemicals recover in a single year using these techniques. Our humble goals are to convert 5 million acres of farmland to the regenerative method by 2025; to demonstrate a 5 to 10 times gain by the farmers as they become profitable and independent in their revenue streams again; and to leave behind the crop insurance and welfare programs we currently have in place for American farmers that also kill soil. We’d like to give the financial and economic future back to these farmers, and in the meantime save the planet through a reduction in toxic spraying, a restoration of the health of our waterways, and a recovery of microbiota within multiple ecosystems.

Sources for Learning More

Fermentation editors Jean Denney (Group Editor) and Caitlin Wilson (Senior Managing Editor) are interested in the ways fermented foods and beverages have potential to heal and restore the body and to help people maintain optimal health.

Published on Feb 11, 2020


Inspiration for edible alchemy.