The Root of Autoimmune Disease can be Found in the Gut


Originally published on: November 8th 2019

The following excerpt is from Dr. Cowan’s book Vaccines, Autoimmunity, and the Changing Nature of Childhood Illness (Chelsea Green Publishing, September 2018) and is reprinted with permission from the publisher

Thanks to the Human Microbiome Project, we know that the human body contains about two to six pounds of microorganisms and that according to some estimates these microorganisms out-number our own cells by as much as ten to one. Other estimates put the number lower, but the fact remains that we are home to trillions of microbes, the largest number of which are found in our gut. And while the mapping of the microbiome is complex and not yet finished, we know that diversity is everything. As in agriculture, diversity tends toward a state of health and balance; monoculture tends toward one of sickness and disease.

Starting in our nose and sinus passageways, and extending all the way to the anus, our gastrointestinal (GI) tract is filled with an incredible diversity of bacteria, viruses, fungi, and sometimes larger organisms. The GI tract can be thought of as a long, hollow tube, divided into different sections, each with a different function. The entire tract is covered with a layer of microorganisms, as well as a layer of hairlike protrusions called villi. Microvilli are similar and have some of the same functions, but can also be found in some other parts of the body, such as white blood cells.

Like our gut flora, intestinal villi (and microvilli) are critical to our health. On the one hand, they enable good absorption of nutrients from the food we eat. Increasing the surface area of the intestinal wall, the villi absorb nutrients and deposit them in the capillaries that lie just below, eventually delivering them into circulation for use as the building blocks of our cells and tissues. The intestinal villi also create tight junctions that result in the selective permeability of the gut wall, preventing proteins, toxins, and other molecules from gaining access to the bloodstream. Like a well-constructed brick wall, the bricks (read: plump, healthy cells) fit perfectly next to one another. Underneath the villi is a layer of collagen and then a muscular wall, which provides structure and stability to the GI tract. The muscular wall is responsible for the contractile movement resulting in peristalsis and the ability to defecate. Without it, the remnants of our food would not move down and out, and our digestive system would grind to a halt.

I often tell my patients to imagine their GI system like a healthy meadow. Healthy subsoil will provide the structure and foundation upon which the upper layers rest. This subsoil is the muscular layer of our GI tract. Then there is the topsoil (the villi), the meadow’s nutritive layer; when healthy, this layer provides the nutrients and habitat for the microbial community. In a pasture or garden, a healthy topsoil gives rise to a thick and vibrant grassy layer filled with an incredible diversity of plant life, everything from perennial grasses, wildflowers, and annual grasses to bushes and trees. 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 carpetlike 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. One common way is the failure of a child to go through the birth canal during delivery. Babies are inoculated with the healthy microbes from their mothers’ vaginas during delivery and these bacteria essentially function as the seeds that will grow into a healthy, diverse gut microbiome. Babies born via C-section initially host more of the flora found in the operating room than the flora found in their mothers. As a result, many American babies have compromised microbiomes during infancy due to the lack of microbial diversity and the paucity of healthy organisms that should populate their gut. Or, if a baby does pass through the birth canal during delivery, but the mother’s vaginal ecology is unhealthy due to poor health, chronic antibiotic use, or yeast infections, the child will start life with poor-quality gut flora and thus develop a poor-quality microbiome.

A typical American child is then subjected to numerous other influences that have a negative impact on the formation of a healthy microbiome. One factor is lack of diversity in the family’s diet, especially in the diet of the nursing mother. Another factor is the overuse of antibiotics in medicine and their ubiquitous presence in the food chain. Yet another factor is a lack of foods with healthy bacterial cultures, including lacto-fermented vegetables such as sauerkraut and pickles; and cultured dairy such as yogurt and kefir. These and many other factors, including GMOs and glyphosate (Roundup), create the conditions in which it is the rare modern child who is born with and able to sustain a healthy microbiome. Without a healthy microbiome, like a hillside with no grass, the intestinal villi and microvilli deteriorate, compromising the integrity of our inner ecosystem at the most fundamental (cellular) level.

When a cell is healthy, the cytoplasm is a gel, not liquid, and this is particularly relevant for our intestinal villi and microvilli, as they have such an important role to play in both absorption and interception. This gel state is the result of intracellular proteins structuring the water inside the cell into a healthy, consistently robust structure. (Think of Jello.) Side-by-side cells with healthy intestinal villi and microvilli will prevent toxins and large molecules from gaining direct access to the bloodstream. When the structure and integrity of the cytoplasm are compromised, the cells shrink and lose their connection to one another and gaps start to appear between the cells. Through these gaps, large protein molecules that shouldn’t show up in the bloodstream pass through. Once in the blood, the body must neutralize these large proteins by the production of anti- bodies. These antibodies often cross-react with the body’s own tissue, and when they do, autoimmune disease will commence. In other words, the root of autoimmune disease can be found in the “leaking” gut. And the root of the leaking gut is the contraction of the cells as a result of unhealthy gel formation within these cells.

What factors interfere with this healthy gel formation? In fact, there are many, the main one being the loss of or imbalance in the microbiome. There are other factors that directly compromise the cells, including cellular poisons such as mercury, aluminum, formaldehyde, and some agricultural chemicals, including glyphosate. These toxins, including glyphosate, are found in modern vaccines. This process of intoxication results in shrinkage of the cells. Shrunken, distorted cells are the hall- mark of celiac disease and other autoimmune diseases. This fact is something that modern medicine is just beginning to appreciate: That is, the etiology of autoimmune disease and allergy can be traced back to distortion of cells and damaged villi and microvilli. And this fact is why diets such as the Gut and Psychology Syndrome (GAPS) diet and the Specific Carbohydrate Diet (SCD) that focus on gut health and repairing leaky gut are so crucial in the treatment of autoimmune disease, autism, allergies, and other chronic conditions.

We are born with an inherent “boundary” in our gut that creates a separation between what is allowed into our bloodstream and what should be kept out. Antigens of all sorts, proteins, bacterial products, heavy metal toxins, and agricultural poisons can breach this gut barrier when the gut lining is inflamed or leaky. This breakdown leads to the production of antibodies that further cellular damage. This process is intrinsic to the process of autoimmune disease.

What does all this have to do with vaccines, which are often administered intramuscularly? The underlying autoimmune phenomenon is the same. And, actually, it has been shown that vaccination does have a direct effect on the microbiome and gut permeability even when given intramuscularly, not orally. The precise mechanism of how this happens is unknown, but I believe that anytime you affect the balance of immune response, you affect the largest and most important organ system of immune response that we have–the gut.

Thomas Cowan, MD has studied and written about many subjects in medicine, including nutrition, homeopathy, anthroposophical medicine, and herbal medicine. He has served as vice president of the Physicians’ Association for Anthroposophic Medicine and is a founding board member of the Weston A. Price Foundation. Dr. Cowan is the author of numerous books including Human Heart, Cosmic Heart, Vaccines, Autoimmunity, and the Changing Nature of Childhood Illness, and his latest book Cancer and the New Biology of Water (coming September 24, 2019 from Chelsea Green Publishing).

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of GreenMedInfo or its staff.

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Originally published on: November 8th 2019