Keystone Species: What the Soil Beneath Our Feet Can Teach Us About Human Health
From Soil to Cell: Understanding the Living Systems That Sustain Us
There is something about spending long periods of time in my garden, without the constant noise of everyday life, that gives me space to think. This time feeds my spirit.
No television. No podcast. No endless stream of information competing for my attention. Just the sounds of nature, my hands in the soil, and time to observe the living world. I leave the phone inside and the notifications off just in case.
An entire microscopic world exists under the surface of the garden. Bacteria, fungi, protozoa, nematodes, earthworms, and countless other organisms interacting in ways we are only beginning to understand. And it's constantly changing. Realizing it is it's own food chain is essential to understanding how to relate to and manage it.
The human microbiome is not different. Consistently trying to find equilibrium. What we eat feeds different types of bacteria in our GI tract. An overgrowth or imbalance in one area creates a need for compensation.
I'll use the example a client once gave me. He wanted to know why he became gassy when he ate chili. I asked how often he ate chili. The answer was, once a year around the Super Bowl and by day three of eating from the same pot, it was no longer a problem. His gut microbiota finally caught up with the demand being placed on this once a year event. I suggested eating legumes of some nature, daily, all year round for colon health and it wouldn't happen any more.
His wife thanked me.
As a dietitian, I've spent more than three decades studying the relationship between nutrition and human health. But the longer I work in this field, the more convinced I become that we cannot fully understand human health by looking at the body in isolation. We are integrated biological systems that work in cooperation with one another in one ecosystem; our body
And that brings me to something fascinating: keystone species.
What Is a Keystone Species?
In ecology, a keystone species is an organism that has an unusually large influence on its environment, even when it represents only a small part of the ecosystem. It's not necessarily how many of these organisms exist that matters, but what they do and how many other organisms depend on them. Remove one, and the effects can ripple through the entire biological community.
This same principle applies to the microscopic world beneath our feet and inside our gut. Microorganisms depend on one another to break down organic matter, recycle nutrients, and produce compounds that support other organisms. Some even feed on the metabolic byproducts of their neighbors, a process called cross-feeding. It's an interconnected biological food web, where certain species play especially important roles in keeping the system functioning.
When these critical relationships are disrupted, the ecosystem may lose some of its resilience, or ability to withstand stress and recover. Other organisms can sometimes compensate, but not always. Whether we're talking about soil or our digestive tract, health depends on more than simply having microorganisms present. It depends on what they're doing and how effectively they work together.
What Happens When We Disrupt the Biological Relationships That Sustain Us?
Our industrialized world has become remarkably efficient at controlling environments, producing food, eliminating unwanted organisms, and treating disease. But what happens to the microorganisms we depend upon? Intensive tillage, monocropping, pesticides, antibiotics, certain medications, environmental pollutants, and diets lacking diverse plant fibers can all influence microbial communities. We may not be killing every keystone species outright, but we may be creating environments where these critical organisms can no longer thrive or perform the functions other organisms depend upon.
This is where detoxification enters the conversation. We often think of detox as something we do to the body rather than something the body is already doing for us. But these systems don't operate independently of the microbial communities that influence our metabolism, intestinal barrier, and immune function.
Our gut microorganisms help metabolize dietary compounds, medications, bile acids, and certain environmental chemicals. Certain gut bacteria, including strains of E. coli, produce an enzyme called β-glucuronidase that can reverse part of the liver's detoxification process, potentially allowing some hormones, medications, and other compounds to be reabsorbed rather than eliminated. Disrupting these microbial relationships can change how certain compounds are processed, although the consequences depend on the organisms and substances involved. Detoxification isn't simply about removing something harmful. It's also about maintaining the biological conditions that support the body's natural processes of metabolism and elimination.
Think about that. We spend considerable time discussing what we should remove from our bodies, but how often do we consider whether we're supporting the biological relationships that help keep us healthy? Keystone species remind us that the loss of even a small part of an ecosystem can have consequences far beyond that individual organism. And perhaps nowhere is our tendency to disrupt these relationships more apparent than in the way we manage our soil.
If the health of our soil depends on thriving microbial communities, why would we imagine that human health exists independently of the microbial world around us?
Have We Forgotten That We Belong to Nature?
Modern life has created an extraordinary degree of separation between people and the natural environments that we once occupied daily. We sit in front of computers all day long. Our food travels greater half way across the country or from other countries. Many children grow up with limited opportunities to explore natural spaces, garden, or understand where food comes from.
Meanwhile, agricultural practices have changed the biological environment in which much of our food is grown. The nutrient density has diminished and we the consumer tend to blame the very systems that we support with our food dollars. That's discussion, however, is for another day.
Some of these changes have been promoted as important benefits, including food increased productivity, food security and an easier life for the farmer. I would argue however that intensive tillage, prolonged bare soil, and limited crop rotations from the conventional system can and often does compromise soil structure and biological diversity. Meanwhile we continue to throw more amendments at the problem, further destroying biology rather than asking why the system is our of balance to begin with.
And I wonder how often we consider the consequences beyond the farm.
Not simply the nutrients in our food, but the relationships between the soil, the plants, the environment, and ultimately, ourselves.
Because food is more than calories. And soil is more than a growing medium. Both are part of the living systems that sustains us.
Are We Disrupting the Biology That Sustains Us?
For generations, agriculture has focused largely on what happens above the ground: crop yields, pest control, and production efficiency. But what happens below the surface is equally important. Soil microorganisms drive nutrient cycling, organic matter decomposition, and many of the biological processes that support plant health.
Remember those keystone species? Some microorganisms play particularly influential roles in maintaining the biological relationships that make healthy soil function. They interact with other organisms, influence nutrient availability, and help shape the microbial communities surrounding plant roots. When we change their environment, we may also change the conditions that allow these important relationships to exist.
Intensive tillage disrupts fungal networks and soil structure. Monocropping limits the variety of plant roots and compounds available to feed soil microorganisms. Prolonged periods of bare soil reduce the continuous supply of carbon that living roots provide. Certain agricultural chemicals can also influence microbial populations, depending on the product, application, and environmental conditions.
But agriculture doesn't have to function this way.
The growing body of research on regenerative agriculture is especially interesting. Improvements in soil structure, water retention, and biological activity are increasingly documented, although results for crop yields and nutrient density vary across farming systems and conditions. Regenerative agriculture at very least attempts to maintain microbiome of the soil which then makes the nutrition already in the soil, plant available. Without the biology our plants are less nutritious.
Soil is a living biological system, not just a medium for delivering fertilizer to plants.
Restoring Microbial Diversity Takes Consistency
Here's something I find particularly interesting as a dietitian: soil and gut microorganisms both respond to what we consistently feed them.
In the garden, different plants release different compounds through their roots, known as root exudates. These compounds provide energy and influence which microorganisms thrive in the surrounding soil. Greater plant diversity can support a wider range of microbial interactions, while organic matter provides additional food and habitat.
Our gut responds to dietary patterns in a similar way. Different microorganisms specialize in breaking down different dietary fibers and resistant starches. As they ferment these compounds, they produce metabolites, including short-chain fatty acids such as butyrate, that support intestinal function and influence immune signaling.
And this is where keystone species become particularly interesting.
Some gut microorganisms help initiate the breakdown of complex dietary fibers that other organisms cannot digest on their own. The compounds they produce become food for neighboring microbes. This cross-feeding helps sustain the larger microbial community.
For example, Ruminococcus bromii is recognized as an important organism in resistant starch degradation. By breaking down resistant starch, it can make fermentation products available to other microorganisms. Its influence extends beyond its own activity because other members of the community benefit from what it does.
One organism's work can help sustain an entire network of microbial relationships.
Remember my client who only ate chili once a year? His digestive system wasn't necessarily malfunctioning. It was responding to a sudden dietary change. Regularly incorporating legumes and other fiber-rich foods can help the gut microbial community adapt to those foods, although gas production also depends on the amount eaten and individual digestive physiology.
We cannot expect microbial communities to flourish if we only provide the conditions they need occasionally.
Whether we're growing vegetables or supporting our intestinal microbiome, consistency matters. Diversity matters. And perhaps most importantly, the environment we create influences which organisms thrive and whether they can perform the functions the larger ecosystem depends upon.
What Happens When We Put Our Hands in the Soil?
There is another dimension to gardening that goes beyond growing food.
Every time we work in healthy soil, we encounter a remarkably diverse microbial environment. Researchers are increasingly investigating how exposure to environmental microorganisms may influence immune development and regulation.
This is part of what scientists describe as the biodiversity hypothesis: the idea that reduced contact with diverse natural environments may contribute to changes in our microbiomes and immune function. The same ecological principles that help us understand keystone species also remind us that microorganisms don't function independently. They exist within communities shaped by their environments.
That doesn't mean getting dirt on our hands automatically improves our gut microbiome or introduces beneficial keystone species into it. The research hasn't established that. But it raises important questions about what we lose when we become increasingly disconnected from the natural world.
And, gardening encourages movement, time outdoors, sensory engagement, opportunities to reduce stress, ground and sun exposure. It also gives us something increasingly uncommon: direct involvement in producing the food that nourishes us.
From Soil to Cell: It's All Connected
We often discuss nutrition, agriculture, environmental health, and human disease as though they are separate subjects. I remember working in the hospital and asking my direct supervisor if the dietitians could get credit for community outreach while working with the local community gardens. The response was and I quote, " What does gardening have to do with health?"
The dogma runs deeeeep.
And perhaps the concept of keystone species helps us understand why.
In both soil and the human gut, certain microorganisms can exert an influence far greater than their numbers suggest. Their activities support other organisms, shape microbial communities, and contribute to the biological processes that keep these ecosystems functioning. When we disturb these relationships, the consequences may extend well beyond the organisms directly affected. This is the very reason why these bacteria are so difficult to isolate and reinoculate a host human. They function within a system rather than in isolation. They perish outside their natural environment.
These relationships are complex. Healthy soil doesn't guarantee a healthy gut, and microbial diversity alone doesn't guarantee good health. But understanding these connections challenges us to think beyond isolated symptoms and individual interventions.
Perhaps the question isn't simply what we need to add to improve our health, but what biological relationships we need to stop disrupting.
That's the bigger lesson I take from keystone species.
Health isn't created by one organism working alone. It emerges from the relationships among many organisms and the environments that sustain them. Improving our health doesn't always begin with another supplement, another medication, or another complicated protocol. It begins by restoring our relationship with the living world.
Plant a seed. Protect the soil. Grow food. Feed the microorganisms that make life possible.
We don't have to understand every microscopic interaction to recognize that we are part of something much larger than ourselves.
Grow something. Grow anything. Your health depends on it.
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