Soil and the Gut: Two Ecosystems with a Deep Connection

Soil and the Gut: Two Ecosystems with a Deep Connection

Nature is full of parallels and deep interconnections. Consider the gut, for example.

The gut, or gastrointestinal tract, comprises the mouth, esophagus, stomach, large intestine, and small intestine and is essentially a long tube through which food travels after we consume it. It doesn’t seem like this collection of organs could possibly have a connection to soil, but it does—a deep one, in fact.

In the GI tract, food is digested by a variety of acids, biles, and other digestive juices, but it’s also digested by a plethora of microscopic organisms that the gut, especially the small and large intestines, plays host to. The exact makeup of this microscopic ecosystem—referred to as the gut microbiome—varies from individual to individual, but in a thriving, healthy mammal, it should be diverse and plentiful. The gut microbiome affects many of the body’s systems, including, of course, the digestive system, but also the immune system, endocrine system, and even the neurotransmitter system—meaning the makeup of your gut microbiome can have a direct affect on mood, mental health, and physical well-being. The population of the gut microbiome is affected by the food you eat, beverages you drink, and medications you take. Antibiotics, even those taken to treat specific ailments, often have the unintended consequence of destroying healthy and essential gut bacteria in addition to the malign bacteria they’re meant to kill.

What does all this have to do with meat, ranching, and agriculture? Quite a lot!

First, there’s the obvious: the higher quality your food, the more beneficial it will be to your gut microbiome, because what you eat, the bacteria in your gut eats as well. But as with most things in nature, the connection goes way deeper than that.

Soil Has a Microbiome, Too

Ecosystems are way more complex than they may look from just a cursory glance. Take a piece of grassland, for example. The grassland’s ecosystem includes the grasses, the livestock that graze those grasses, and other animals that live in those grasses, but it also includes a plethora of lifeforms we don’t often think about: insects, fungi, and millions and millions of microscopic organisms that live in the soil. One gram of soil contains 40 million individual bacterial cells, and a milliliter of fresh water contains at least a million. Bacteria are the most plentiful organisms in any ecosystem. In fact, they’re the most plentiful organisms on earth.

Our current agricultural system of monocropping and conventional grazing, however, is not ideal for the propagation of the soil’s microbiome. Just like these practices are detrimental to the visible parts of the grassland ecosystem, they’re destructive to the invisible parts as well.

Diversity Is Key

If you eat only one food, the bacteria needed to digest that food will flourish in your gut, but most or all other bacteria will die. If you later introduce another food into your diet, the result will be uncomfortable at best. For one thing, the bacteria needed to digest that new food may not be present, and for another, any new bacteria you introduce with that new food is not going to cooperate well with the rest of your gut’s ecosystem—at least not in the short term.

Similarly, using a plot of soil to grow only one crop means that the microbiome of that soil will not be as diverse as it could be.


Additionally, just like taking antibiotics kills good bacteria in the gut as well as bacteria that causes illness, pesticides like glyphosate kill essential soil microbes (in fact, glyphosate is patented as an antibiotic). All this mismanagement has led to a situation where most of the earth’s soil is so depleted that we may have fewer than 60 harvests left.

Even Deeper

We’ve covered the parallels between the gut microbiome and the soil microbiome, but nature is about more than just parallels. In nature, everything is connected. Believe it or not, the quality of our soil’s microbiome directly affects the quality of the gut microbiome in a number of crucial, surprising ways.

First, let’s return to the above point about diversity. Yes, diversity of the soil microbiome operates similarly to diversity in the gut microbiome, but diversity in the soil microbiome also directly affects diversity in the gut microbiome. Poor-quality soil leads to less nutritious crops. In some ecosystems, for example, legumes work with a specific soil bacteria to mineralize nitrogen in a way that makes it bioavailable to the rest of the plant community in that ecosystem. So, in those ecosystems, without the bacteria, or without the legumes, the whole ecosystem suffers. Poor soil quality also leads to less nutritious grasses, which affects the gut microbiome of ruminants who graze on those grazes, and as we’ve covered, the quality of the microbiome affects health in a number of ways. Thus, if we don’t pay attention to the quality of our soil’s microbiome, even the meat we eat will not be as nutritious as it could be.

But here’s where things get startlingly freaky, because the connection between the soil microbiome and gut microbiome runs even deeper than we’ve covered so far. DNA sequencing has found that bacteria in soil swaps genetic information with bacteria in the gut via a process called horizontal gene transfer. Scientists refer to this as a “gene network,” and it’s massive: 10,000 unique genes are regularly transferred between 2,234 bacterial genomes, and this transfer happens across species. This process is how antibiotic-resistant superbugs are created, but it’s also essential for the proliferation of healthy bacteria in both the gut and soil. Of course, glyphosate interferes with this process by killing good bacteria. And, perhaps worse, genetically engineered foods introduce genetic information into the ecosystem that isn’t necessarily meant to be there. 

Stunning Complexity

The complexity of the soil microbiome, and the way it affects the health of all other creatures in the ecosystem and the food chain, is simply stunning. Soil microbiomes are hyper-local, meaning the bacteria population in one plot of soil can be completely different from the population in a plot of soil even a few thousand feet away. One study found that the soil at the foot of Washington’s Rattlesnake Mountain is notably different from the soil found at the top, just 3500 feet away.

The health of most of the planet’s soil is currently in dire straights. While we can attempt soil transplants to improve one location’s microbiome by introducing bacteria from another location’s (similar to a fecal matter transplant, which is often used to improve the microbiome of unhealthy human digestive systems), that would only be addressing the symptoms, not the underlying problem.

Only by changing our agricultural system, by reverting to a system in which all organisms in an ecosystem—a diversity of plants, animals, insects, and microorganisms—are recognized as crucial to the survival of the ecosystem, can we ensure that our soil, crops, animals, and even our digestive health, will thrive.