Moving in and through these grassy plant layers are insects, butterflies, and animals that together create the diverse ecosystem we call a meadow. While meadows may look static, they are, like our gut, teeming with life.
Our gut lining is also home to a diversity of microbial life, forming a carpet-like inner lining of the gut, lying on top of the plump, healthy cells with healthy villi, and supported by the blood vessels and muscular layer of the gut wall. When healthy—whether a meadow or our gut—the various layers work together to create health for the entire ecosystem. This is the basis of resilience, a state of balance and health that accommodates disturbances without compromising the integrity of the whole system.
In our gut, the feedback system of these layers working together enables microbes to synthesize nutrients that are as important to our well-being as the nutrients provided by our food. The gut microbiome has many more functions, such as aiding digestion, providing bulk to the stool, keeping pathogens in check, and perhaps others we have yet to discover.
When intact, these well-functioning layers—in a meadow or in our gut—prevent the absorption of pathogens—a word I’m using to mean anything, including toxins and agricultural chemicals, that causes disease—into the underlying layers. In a meadow, the rich biodiversity and various soil strata help to prevent toxins or agricultural chemicals from reaching the groundwater. Much will be caught and retained by plants and grasses. If this first layer of the meadow is breached, humus in the soil will bind toxins so they can be digested by the worms, fungi, and other organisms in the topsoil. If the topsoil is breached, then the subsoil will act as a physical barrier to prevent the toxins from reaching the groundwater. Of course, toxins will reach the groundwater in plenty of instances; when you overload a system with toxins, it loses its resilient capacity to absorb, integrate, and maintain homeostasis.
When we are healthy, enzymes in the mouth, acid in the stomach, and microbes in the lower gut will often destroy pathogens. If a pathogen escapes these first lines of digestive defense, then the villi will prevent their access to the bloodstream. If the villi are compromised, we have the physical barrier of the smooth muscular layer of the intestinal wall. In health, these systems function together to screen pathogens from the bloodstream.
They are, in essence, guardians of our health. On a more metaphysical level, the gut ecology is the preserver of our integrity. We are not supposed to be a teeming collection of unwanted toxins, proteins, antigens, and pathogens floating around in our blood and settling in our tissues any more than groundwater is supposed to be contaminated with toxic agricultural products. When this contamination happens, we set the stage for the onset of autoimmune disease, one of the predominant plagues of modernity. A loss of diversity of the microbiome can happen in a number of ways.