The Soil Inside

There is a psycho-spiritual teaching that what is outside is inside. It is often used to mean that when we look at the world we see it through the lens of the organizing principles by which we simplify a natural world that would otherwise overwhelm. Like most popular teachings, it reflects a literal truth: the bacteria that live in the soil around us also live in our gut.

Our microbiome includes the flora that live in our mucous membranes, lungs, skin, and gut. It is symbiotic, that is, we provide an environment in which it can thrive, and it protects us from infections and produces essential nutrients such as vitamin B12. It also helps to digest our food. Without a healthy normal flora, we cannot eat, live or thrive. This means that if we destroy our flora with antibiotics, or if our parents have unhealthy gut flora, or if the soil around us is unhealthy, we, too, will be unhealthy. This means that our health is inseparable from the health of the natural world.

Our scientific understanding of the body is still very limited. We know very little about the autonomic nervous system or the gut. Fortunately, soil scientists who are beginning to study the living soil are developing methods that doctors can use to study the night soil in our gut. In the mean time, we can empirically aid our symbionts by eating organic and biodynamic foods, eat healthy living cultures, and take probiotic supplements. We can emulate indigenous peoples who bury themselves in wild soils and even try eating the proverbial peck of dirt that enhances our flora as toddlers and that may be safe in adulthood. We can respect our microbiome and at least try to care for it as well as it cares for us.

When I learned that eating was the source of all my symptoms, I knew that my body’s reaction to food was a part of the problem. An allergist had tested my blood and found circulating antibodies to tomatoes, nuts, and other foods, and elimination diets had eased my symptoms. But there was at least one other possibility that no one could test: I might have been treating the wrong patient. It may be my microbiome that is sick and not my human flesh.

had done many things that might have damaged my microbiome. I had had at least one parent with an unhealthy microbiome; had been raised away from healthy soils on a diet of chemically farmed foods; had grown up equating cleanliness with sterility; had worked in a bacteriophage research laboratory; had taken many courses of antibiotics; had radically changed my diet; had traveled; and had been exposed to countless chemical and biological agents, including those circulating in day care centers and hospitals. Since my first pregnancy I had experienced chronic gastrointestinal difficulties that seemed to vary with diet, medical treatments, co-infections, and travel. I had every reason to believe that my microbiome was a key cause, or the only cause, of my predicament.