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Decades ago, prior to the Human Microbiome Project, the brilliant, iconoclastic, eco-farmer, Bob Cannard, stood up in public and made the seemingly outrageous announcement that the human body was, in fact, an amalgamation of microbes. The skepticism in the room was palpable and the derision was audible.

But now science has confirmed that microbes in and on our bodies outnumber human cells by estimates ranging from 3-1 to 10–1. And that microbial community, now known as the human microbiome, plays vital life-supporting roles in many of our bodily functions, including digestion, immunity, and hormone and blood sugar regulation.

 As a farmer, Canard works diligently to optimize what he refers to as the “digestive capacity of the soil.” When I first heard him make that reference, I thought it was an enigmatic and imprecise metaphor for soil fertility, but, in fact, it’s an insightful and scientifically accurate way to describe the interactions within the soil food web, in which microscopic organisms play an outsized role in decomposition, nutrient cycling and plant health. Diverse species of microbes digest and break down organic matter making it more digestible for the next level of the soil food web, ultimately converting it into a form able to nourish plants. Microbes are also architects: they create soil structures that increase the water retention capacity of the soil and enhance carbon storage.

Whether it be fertility-enhancing activities in soil, or the critical functions of fighting disease and regulating metabolic functions in the bodies of humans, it turns out that our lives are highly reliant on the skillful, mutualistic activities of invisible organisms.

The Astonishing Microbes

Though invisible to the naked eye, microbes make up almost 25 % of the weight of all life on Earth. There are hundreds of millions to trillions of species of microorganisms (more than 99% of them undiscovered!) that perform vital functions sustaining life. The cyanobacteria that live on the oceans’ surfaces generate oxygen and help regulate atmospheric CO2. Several types of bacteria and fungi help control the nitrogen cycle in the atmosphere and in soil. As the oldest life forms, microorganisms have an astounding ability to adapt to most all of life’s extremes. Some actually have evolved to thrive in ponds of nuclear waste.

Their ubiquity is also impressive: they colonize virtually all natural surfaces, so it should come as no surprise that microorganisms have evolved symbiotically with humans and inhabit heathy soils in abundance. Microbiomes found in different ecosystems from land to sea, or on and in the bodies of people, animals and plants, could be considered sophisticated civilizations, without which much of life would be severely degraded, if not cease to exist.

The Human Gut Microbiome: An Ancient Community of Allies

Microorganisms, the oldest life forms on earth, have been around more than 3.5 billion years, and over the last 6 million years, they have used humans as an opportune host with which to establish a complex, symbiotic relationship in which each entity has grown to depend on the other to survive and thrive.

But it wasn’t until 350 years ago–a relatively fleeting interval of time compared to the billions of years of microbial life and the two or so million years since early humans first appeared–that the first crude microscope enabled the human eye to view these minute life forms.

150 years after the advent of the microscope, the 19^th century French chemist Louis Pasteur discovered that microorganisms are the cause of infectious diseases. That discovery became known as the germ theory, and it ultimately led to the development of wonder drugs to fight infections. But the germ theory is only part of the story of the relationship between humans and microbes. It was not until relatively recently that the health-regulating functions of microorganisms in the human body became known, and the failure to understand the positive role of microbes and the critical importance of the microbiome as an essential aspect our immune system has led to some unintended consequences.

Unfortunately, it has become widespread practice to use antibiotics in livestock on a massive scale as a strategy to prevent disease rather than limiting them to the more judicious use for curing infections. Also, doctors, over the years, have overprescribed antibiotics in people when they were not necessary. Both these misguided practices have contributed to the dangerous crisis of rising antibiotic-resistant bacteria, as these dynamic organisms adapt and become immune to medications. Microbes are some of life’s most dynamic “shapeshifters.” They have an average lifespan of 12 hours, which gives them countless generations to evolve and become resistant to many of the formerly life-saving drugs.

Overprescription of antibiotics also leads to a reduction in both the number and the species of the beneficial microorganisms in the gut. Many antibiotics don’t differentiate between infectious and benign organisms. Those misguided practices arose out of an overemphasis of the germ theory and a lack of understanding of the microbiomes of humans and animals.

Good Health is Dependent on a Healthy Microbiome

Although there were some isolated discoveries of the healthful benefits of good bacteria going back to the late 1800s, those ideas were carried forward mainly on the fringes by traditional cultures and modern aficionados of probiotic health foods such as kimchi, miso, yogurt, kefir, etc. It wasn’t until the Human Microbiome Project in 2007 that science fully accepted the critically important role of the microbiome.

Before that, the colon was viewed as nothing more than a cesspool for housing undesirable microbes and temporarily storing metabolic waste. But more and more, science has been discovering how important a role the microbiota in our gastrointestinal tracts play in the regulation our health. The vast majority of our microbiome reside in the colon where a significant portion of our immune system is also located.

Two-way communication between microbes and our human cells and organs takes place via the immune, endocrine and nervous systems that form an intricate network that regulates our metabolic functions. The science is not exact, but of the trillions of microbes that make up the human biome, only about 1400 are considered potentially pathogenic, so wiping out good bacteria unnecessarily with antibiotics can take a serious toll on a person’s long-term health.

The relationship between our bodies and our microbiome is so intimate that bacteria even share genes with us in a process known as horizontal gene transfer, a kind of intercellular sex sometimes referred to as “jumping genes.” And that transfer is not trivial, it happens among millions of genes. The gut microbiome plays a crucial role in metabolism, immunity, maintaining a balance in our intestines between fighting pathogens while regulating inflammation, and even influences brain function and behavior.

A disruption of the makeup of the microbial community by poor diet, exposure to toxins, lack of exercise, etc. can lead to disease. One example is obesity, which creates a favorable environment in the gut for a specific strain of bacteria to flourish and produce endotoxins that leak into the bloodstream and trigger a chronic state of inflammation. Research has shown that chronic inflammation can result in a cascading suite of misery: diabetes, heart disease, some cancers and many other chronic degenerative diseases. Even some psychiatric disorders are now being linked to poor gut health. Approximately 60% of those who suffer from gastrointestinal disorders suffer from one of several psychiatric disorders, such as depression and anxiety.

Perhaps Bob Canard’s assertion that we are essentially an amalgamation of microbes was a bit overstated, but not by much. It’s now well established that our bodies are an ecosystem rife with complex, mutualistic relationships with microorganisms that have co-evolved with humans to support robust health.

Healthy Soil is Alive with Invisible Allies

Another critical microbiome, not just for people, but also for animals, plants and ecosystems is the microbiome of the soil.

What Cannard refers to as “soil digestion” actually begins one level above the microbiome with the soil macro fauna–those organisms that can be seen–such as earthworms, sow bugs, beetles, ants, etc. Those two communities taken together are referred to as the “soil food web.”

The macro fauna, along with fungi–an important part of the microbiome–initiate the first cycle of decomposition breaking down carbonaceous material, leaving behind a metabolic biproduct (their waste) that microorganisms feed on. Bacteria and other microbes ultimately solubilize the nutrients, converting them into a form that plant roots can take in.

Plants uptake nutrients in a few different ways. To a limited extent, they reach out into the soil and intercept nutrients that have been solubilized by microorganisms. Nutrients can also be carried by water in the soil to the root zone known as the rhizosphere. And plants also get fed with the assistance of mycorrhizal fungi that attach to plant roots, extend out into the soil and harvest water and nutrients and deliver them to the plant.

Plants have the extraordinary ability to take carbon from the air, hydrogen from water molecules, and, by using sunlight as an energy source via photosynthesis, to produce food in the form of carbohydrates that feed not only themselves but also their microscopic allies in the root zone. About 30 % of that food is pushed out into the soil through their roots to feed beneficial soil microbes.

Recent research has revealed just how intimate a relationship plants have with their microbiome. Dr. James White of Rutgers University has discovered a process called the rhizophagy cycle, a fascinating process in which plants actually draw microbes into their roots and circulate them until they break down into nutritional components the plant can absorb. If the process stopped there it would seem a bit exploitive and ungrateful by the plant toward its crucial partners, but it doesn’t stop there. Not all of the microbes taken into the plant are broken down and consumed. The survivors are pushed back out into the rhizosphere to repopulate their community, and in a gesture of gratitude the plant sends a renewed supply of food to those microbes to ensure they can, in biblical terms, “Go forth and multiply” and renew the cycle. The drama of life, death and renewal even occurs at a microscopic level.

 All of these ways in which plants get food are directly or indirectly associated with microbes. Photosynthesis provides plants with the macro nutrient of carbohydrates, but for the critical micronutrients that play an essential role in their health and immunity–and subsequently for the well-being of those who eat the plants–they rely on the services of the soil microbiome.

And, as in the human microbiome, those services are comprehensive: communication with cells, turning genes on and off, warding off pathogens by opposing them directly or by stimulating the plant’s innate immune response, etc. And that’s just a partial list, in fact, we still don’t have a complete understanding of all the interactions of plants and microbes. We haven’t even identified the majority of species in the soil microbiome. What we do have is a better understanding of the highly elegant and cooperative system that has stood the test of time to the tune of millions of years by refining its ability to create a steady-state fertility cycle.

As soil microbiologist Dr. Kris Nichols said in an interview that I conducted with her, “Mycorrhizal fungi have been associated with plants for over 400 million years, so they have been able to figure out how to optimize the system and are able to do it at the highest level of efficiency… Humans can’t do it better.”

Misguided Progress

In contrast, the Green Revolution, for which its founder Norman Borlaug won a Nobel Prize, is less than 100 years old. Its celebrated contribution was high-yielding seeds for food crops that came with a promise to feed the world, but the caveat is those hybrid seeds require high amounts of chemical fertilizers and pesticides. Most people are at least somewhat aware of pesticides’ profound “side-effects” on human and ecosystem health, but they’re generally not as aware of the negative impacts of chemical fertilizers.

The routine over use of high amounts of nitrogen and phosphorous causes those fertilizers to runoff off farms and leach into waterways that ultimately create “dead zones” in seas all over the world. As they runoff from farms when it rains, the fertilizers leach into waterways that make their way to rivers that drain into the oceans. The Mississippi River, for example, is estimated to carry 1.7 million tons of those chemicals into the Gulf of Mexico each year, resulting in giant dead zones in that body of water. That is a serious consequence at the macro level, but how do chemical fertilizers affect the soil microbiome?

Commercial chemical fertilizers contain abundant amounts of macro-nutrients—nitrogen, phosphorus, and potassium, but for the most part they lack the valuable micro-nutrients that are also essential for heathy plants, animals, and people. Once applied to the root zone those highly soluble fertilizers are readily taken up by the plant roots. Plants get bigger but often have lower nutrient density. The intervention of adding highly stimulating inputs disrupts a natural cycle and is damaging to the microbiome in two ways. First, the flush of nitrogen pushes the microbes into an overstimulated reproductive and feeding frenzy that ultimately causes the microbial community to crash. The second is a direct disruption of the millions of years of coevolution and symbiosis between plants and microbes. When plants are fed with chemical fertilizers, they turn their back on their traditional community and ultimately decide not to expend the energy to feed the soil microbiota, further degrading the highly efficient, mutualistic system of self-sustaining fertility. At that point, the only way to keep producing crops is to keep pumping them up with more overstimulating fertilizers that increasingly impoverish the soil, degrade the nutritional vitality of the plants, and toxify the global environment.

 As David Montgomery and Anne Biklé  wrote in their fascinating book The Hidden Half of Nature, on the topics of soil and human microbiomes,“The more farmers rely on synthetic inputs instead of  beneficial soil life, the more they need the former and lose the latter.”

Regenerative agricultural is emerging as the response to the degradation of soil health caused by chemically-driven industrial agriculture. By farming in a way that mimics natural systems, regenerative farmers prioritize soil health rather than agrochemical inputs to create a thriving, productive farm for the long term. The first step in accomplishing that is by learning how best to work with the invisible microbial partners in the soil and learn to be a good ally rather than an antagonist. That is the prudent and most scientifically practical way to maintain agricultural soil health and productivity and ensure long-term food security.

The Relationship Between Soil and Human Microbiomes

Science is in the process of an ongoing exploration of the enormous importance of these two fascinating microbiomes. We now know that we are vitally dependent on healthy microbiomes for human and ecosystem health, but less is known about how, or if, these microbiomes are related.

 Soil, for billions of years, has been the greatest reservoir of microbial richness while the human microbiome is at best a few million years old. Over those millions of years, humans evolved predominately in rural environments in which they were very much integrated in nature. It would seem logical, under those circumstances, that the soil microbiome would be a significant influence on the human microbiome, but even though functional parallels between the two microbiomes clearly exist, a direct relationship has not yet been determined.

How then does our microbiome develop in each of us? Not surprisingly, we receive our first  microbial inoculation from our mothers as we pass through the birth canal, have skin-to-skin contact, and are breastfed. Lacking any one of those leaves a new born with a less vigorous microbiome to start life with. As children grow, the environment plays a big role in the further development of their microbiome. Locale, ecosystem, diet, lifestyle, etc. all have a direct influence in the makeup of our microbiota. In fact, each person’s microbiome is so individualized that it is sometimes compared to the distinctiveness of fingerprints.   

Microbial life is highly dynamic and adaptable. In hunter gather cultures, for example, when a deer or other animal was hunted down, it was carried back to the village to share with family and community. Carrying, butchering, and cooking the meat all involved lots of physical contact with the animal. Some of the animal’s microbes were inevitably transferred to the people involved in those activities.

Conceivably, if the conditions were right, those microbes could become part of that person’s microbiome. Similarly, a transfer of microbes from nature to people could occur with early farmers and even small farmers today who have regular physical contact with their environment. That kind of contact, with our hypersensitivity to “germs,” could raise alarms of contracting disease from animals or soil, etc. But remember, the vast majority of microbes are not just harmless but are life-supporting and protective against disease.

Multiple studies in Europe and North America have shown that kids who grow up on farms or in rural areas and have regular contact with soil and animals have fewer allergies, asthma and auto immune diseases. Even in households with pets, kids have better immunity than those who don’t live with a four-legged companion.

As a research article from the University of British Columbia, “Linking the Gut Microbial Ecosystem with the Environment,” states: “Reduced exposure to pathogenic microorganisms, largely as a result of modern hygienic practices, can also result in defective immunoregulation.” 

This speaks to the overuse of antibiotics when not necessary and the over-sterilization of non-medical environments. A microbiome rich in diversity can protect against disease, and when stimulated by pathogens, it can learn how to defend against that specific disease. Of course, there are times when medical interventions such as antibiotics are absolutely necessary, but our first line of defense is a strong immune system developed by interaction with nature and a healthy diet and lifestyle.

The analogy in regards to the soil is the disruption of the microbiome by chemical inputs that degenerate the health of the entire food chain from soil to plant to person or animal.

In The Hidden Half of Nature, Montgomery and Biklé wrote: “Pesticides and herbicides have also altered soil microbiota in ways we do not fully understand. Some studies, however, point to the effects that echo the basic problem with the Western diet–like overconsuming refined carbohydrates, excessive use of agrochemicals feeds the bad actors and starves the good ones.”

A highly diverse, well-balanced community of predominately beneficial microbes is the key to both personal and soil health. A core tenet in seeking to preserve an ecosystem’s biodiversity is to maintain, not only a large number of organisms, but a wide array of species. That combination is the foundation for establishing resilient health in the soil as well as the human microbiome.

Our connection to nature is often overlooked or undervalued. As we degrade biodiversity in nature, it could well come at a cost to human health. In the aforementioned article “Linking the Gut Microbial Ecosystem with the Environment,” the authors hypothesize that: “Urban development leading to the loss of local habitats and biodiversity may be detrimental to human health by depleting or otherwise altering the reservoirs of environmental microbes.”

Hopefully, we can now agree that the unintended and indiscriminate depletion and destruction of microorganisms is just not a good idea. We could be eliminating lifeforms that have been our indispensable allies for eons. Modern science is just scratching the surface of our understanding of these sophisticated, invisible civilizations that we have evolved with and depend on. And as Bob Cannard implied, those microscopic life forms are much more an intimate part of who we are than we previously could have imagined.