Listen to your gut: Importance of the microbiome

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The human body is teeming with life. It is almost incomprehensible to imagine the immensity of collective effort that is necessary for everyday function: for drinking and digesting coffee in the morning, for walking up the stairs, for dreaming, for dancing, for breathing. We are not autonomous. Rather, we are an invisibly unfathomable wilderness of organisms.

The microbiome is a critical part of this complexity. It is a tiny world with a density equal to that of a mango, yet it contains more than 100 trillion microorganisms. These microscopic little beings, including prokaryotes such as bacteria and archaea, fungi and even viruses, are the miniature cogs in the mechanisms of important processes such as decomposition, nitrogen fixation and digestion. 

The warm, rumbling insatiable stomach provides a home for a part of the human microbiome that is gaining a lot more attention from scientific and cultural communities: the gut microbiome. The gut microbiome alone encodes about 150 times more genes than the entire human genome. The immensity and complexity of this system is ‘sublime,’ a philosophical aesthetic that represents the feeling of grandeur beyond translation and emulation. You would need a hundred times the stars in the Milky Way galaxy to equal the number of microbes inside of a single human body. 

The gut microbiome alone encodes about 150 times more genes than the entire human genome.

Yet aesthetics and landscapes of the sublime can be manipulated by human interference. At birth, a baby’s gut microbiome is informed by the microorganisms inside of the mother’s birth canal and in breast milk. After that, according to the Harvard School of Public Health, “environmental exposures and diet can change one’s microbiome to be either beneficial to health or place one at greater risk for disease.” 

According to American author Michael Pollan, Knight Professor at the UC Berkeley Graduate School of Journalism, “while your inherited genes are more or less fixed, it may be possible to reshape, even cultivate, your second genome,” which is a “humbling new way of thinking about the self.”

An individual’s microbiome is thus incredibly specific, based on lifelong habits and genetic particularity. Gut health is intricately tied to the body’s immune system. Hsin-Jung Wu and Eric Wu in “Gut Microbes,” explain that microbes benefit their host “…in many ways, including, but not limited to, digestion, production of nutrients, detoxification, protection against pathogens and regulation of the immune system.” What, and how a person consumes is one of the main ways that healthy or unhealthy elements of the outside world enter the body. 

In fact, to see how important the gut is to the immune system, one only needs to look at a cell wall that is only a single layer thick. It is called the epithelial layer and it separates 38 trillion gut microbes from gut-associated lymphoid tissues that contain 70% of the immune system. This thin gut lining is a mode of communication between these two essential bodily systems, and is very sensitive. Without a healthy microbiome, autoimmune disorders can occur: in short, the body starts attacking itself. The body’s defense system and functions are then too weak to prevent other diseases.

So what causes the disruption of a healthy microbiome? Because the system is so sensitive to external stimuli, acting as a filter for consumption and exposure, the health of the microbiome is easily undermined. 

Without a healthy microbiome, autoimmune disorders can occur: in short, the body starts attacking itself.

Because a child gets their initial microbial head start during vaginal birth, the nature of the birth is one of the ways in which gut disruption can occur. Caesareans (in which the child is cut out of the mother’s stomach due to birthing complications), can interfere with the earliest bestowal of a microbiome. So can the lack of human breast milk, which is the perfect nutrient package for human babies, including important prebiotics called HMOs (human milk oligosaccharides) which aid the growth of the developing gut and the immune system.

The increased use of sterile cleaning habits, as well as the increased use of antibiotics, is also harmful. It is true that bad bacteria exist; such as E. coli and salmonella, and antibiotics are sometimes necessary to rid the body of illnesses that align with these bacterial diseases. But the overuse of antibiotics can also work to eliminate good bacteria, including those that reside in the gut. The same can be said of viruses and parasites. There is an unpleasant stigma surrounding these words, especially during a mass pandemic, but viruses, parasites and bacteria are essential to the balance of the gut ecosystem. 

Diet is an element of the microbiome that is deeply integral to the health of the gut microbiome. The type of food and its accompanying vitamins and nutrients that the body ingests provides nourishment for the swarming system of microbes that identify and break down the food. Essentially, all the stuff dancing around in your twisting, pink intestines informs your metabolism. In turn, the food that you eat informs the microbial community. It is essential then, for a variety of richly nutritious food to be consumed. This will generate increased diversity and system resilience of the microbiome. 

Dr. Will Bulsiewicz, a gastroenterologist, explains that stress harms the microbiome. The brain and the gut are in constant communication and can alter each other’s functions. This past year or so, there has been global disruption to our lives. Jobs have been lost, loved ones have been lost and health and wellness seems more fragile than ever before. Stress can be considered a health crisis of its own. It makes the body more vulnerable to disease, and encourages bad habits that expedite disease, such as the consumption of unhealthy food and the increased use of addictive substances. 

All of this impacts the gut, and thus the immune system. COVID-19 infection is compounded by this gut vulnerability. These gut-associated diseases are often caused by the inability of the gut microbiome to properly break down foods and release the essential nutrients necessary for the health of the immune system, brain and entire body. Diabetes, blood pressure, coronary artery disease and diseases of the gut are some of the preexisting conditions that maximize susceptibility to the virus, and these diseases are widespread in the modern world. In fact, according to the CDC, 34.2 million Americans have diabetes, about one in ten. 

Stress can be considered a health crisis of its own. It makes the body more vulnerable to disease, and encourages bad habits that expedite disease, such as the consumption of unhealthy food and the increased use of addictive substances.

According to the American Diabetes Association, of the people with diabetes in the United States (a diet-associated autoimmune disorder) only “7.5% of those with diabetes are non-Hispanic whites, 9.2% are Asian Americans, 12.5% are Hispanic, 11.7% are non-Hispanic Blacks, and 14.7% are American Indians or Alaskan Natives.” 

In comparison to white, non-Hispanic persons, American Indians or Alaskan Natives 2.4 times as likely to die from COVID-19, Asian persons are 1.0 times as likely to die, Black or African American, non-hispanic persons are 1.9 times as likely to die, and Hispanic persons are 2.3 times as likely to die. 

There is a clear pattern that can be seen in the rates of underlying conditions, as well as in the rates of the virus that has been ravaging on for the past year. The lack of equity in the medical system is not the only issue here. 

An element of this that cannot be overlooked is the increased levels of trauma in underrepresented communities as a result of structural racism, violence, disempowerment, the prison industrial complex, colonization, lack of access, forced generational poverty … the list could go on. 

There is a clear pattern that can be seen in the rates of underlying conditions, as well as in the rates of the virus that has been ravaging on for the past year.

Dr. Bulsiewicz says that “the most challenging patients I see as a gastroenterologist are the people who have been victims of physical, emotional, sexual, psychological trauma… They don’t realize the way it affects their gut… eating at them at a subconscious level.” People that have been generationally and currently affected by Western colonialist power dynamics have experienced an inordinate amount of trauma that impacts their quality of life. 

Unfortunately, most of the data that we have collected regarding the microbiome is Western-centric, consisting of gut studies from industrialized countries, such as the Human Microbiome Project based in the United States. But according to Emily Davenport, Jon Sanders, Se Jin Song, Katherine Amato, Andrew Clark, and Rob Knight, “Western microbiomes differ in several ways from the non-Western microbiomes profiled to date. First, Western microbiomes consist of 15 to 30% fewer species than non-Western microbiomes… Second, Western microbiomes lack certain species that consistently occur in non-Western microbiomes.”

Some consider the loss of the microbiome in Westerners a result of industrialization, or the standardization of agriculture, the increased use of preservatives and pesticides and environmental pollution in urban areas. This is considered the “disappearing microbiome hypothesis.”

When one looks at the rates of heart and gut disorders, diabetes, cancers and other major diseases within the Western world, one can draw a direct line from the trauma inflicted on ethnic communities from white colonialists to the disproportionate effects of modern health issues. Nonwhite ethnic communities are usually affected most deeply by the causes that lead to a “disappearing microbiome” environmental pollution, healthy food disparity and the immense wealth and access gaps lead to the issue of the disappearing microbiome. 

The highest rates of diabetes and COVID-19 related deaths are seen in Native American and Alaskan Native populations. This can be directly linked to the confluence of diet and trauma, among other discriminatory and prejudiced confounding factors.

Indigenous people were and are devastated by white colonialism. The gradual and violent Western movement of white Americans was essentially a genocide of the hundreds of Native tribes. 

When one looks at the rates of heart and gut disorders, diabetes, cancers and other major diseases within the Western world, one can draw a direct line from the trauma inflicted on ethnic communities from white colonialists to the disproportionate effects of modern health issues.

The immense loss of many tribes went beyond the nationally endorsed murder of Indigenous people. It was also seen in the forced seizure of land, the vast diminishment of Indigenous holdings and even forced displacement to reservations that were in entirely different areas and ecosystems than the ones around which their culture was centralized. Loss of land was also a loss of food. 

According to the U.S. Census Bureau, there are 6.79 million Native Americans, making up nearly 2% of the US population. They sustain some of the highest rates of diet-related disease and food insecurity. One in every four Indigenous people is food insecure, compared to one in nine non-Native Americans. 

Reclamation and access to Indigenous land needs to be a national priority. There are a few notable collaborative projects between UC Berkeley and Native tribes in California that are trying to reparate the effects of food insecurity. One such project is the Agriculture and Food Research Initiative in the Klamath Basin. The project seeks to “achieve a sustainable food system that results in healthy communities, healthy ecosystems and healthy economies among the Karuk, Yurok and Klamath Tribes and becomes a model for other tribal and rural communities.”

UC Berkeley is working with the tribes in the Klamath area to research their historical and current culturally vital foods, medicines and other resources The larger end goal is to try and reintegrate these resources back into the tribal diet in order to combat food insecurity and diet-related diseases such as obesity and diabetes. Accompanying nutrition and stewardship education within and outside of the tribal community is a top priority so that tribal knowledge and health can be strengthened intergenerationally, and long-term external partnerships, such as the one with UC Berkeley, can be sustained. 

The Amah Mutsun Tribal Band located in the Santa Cruz mountains is another Native tribe that the UC Berkeley archaeology and anthropology departments collaborate with. Berkeley archaeologists are using tactics to try and uncover historic land management practices so that the tribe’s stewardship knowledge can be renewed and enhanced. 

An element shared by both projects is the attempt to try and reintroduce fire to the landscape. Many of the plants that these tribes depend on need fire for reproduction and maintenance. Unfortunately, because of the lack of land and the exclusionary policy of modern fire management, there is slim opportunity for tribes to work with fire. These projects are trying to strengthen tribal access to fire so that fire can continue to be used as a stewardship tool. 

Enhancing food security through the renewal of traditional land practices and increased access to that land is essential to the health of the microbiome. Eating the culturally important foods that have evolved with Native diets for hundreds of years is deeply necessary for both the microbiome and the resilience of Native societies. 

There is also inequality seen along ethnic lines in cities. A modern segregation process called redlining, which is the process of demarcating space for certain communities, leaves communities of color in parts of cities and towns where there are less resources, such as access to healthy food. Food deserts are considered places where people live more than a mile away from a supermarket, a natural foods store, or a farmer’s market, where there is access to affordable fruits, vegetables, and other necessary items. More than 19 million people live in food deserts. 

A modern segregation process called redlining, which is the process of demarcating space for certain communities, leaves communities of color in parts of cities and towns where there are less resources, such as access to healthy food.

These ‘food deserts’ are disproportionately located in low-income areas, and the majority of people who are pushed into low-income areas due to a host of inequitable reasons, are non-white. In Oakland, for example, areas with higher Latinx populations do not have nearby grocery stores. The American Journal of Preventative Medicine says “studies have found that wealthy districts have three times as many supermarkets as poor ones do, that white neighborhoods contain an average of four times as many supermarkets as predominantly black ones do.” In impoverished communities, fast foods and corner store snacks are both cheaper and more accessible. The lack of a complex and healthy diet, paired with the stress of poverty, is a recipe for disaster on behalf of the microbiome, and thus, the immune system.

The reconfiguration of our cities, and the equitable placement of community gardens, green space and food stores also needs to be a national priority, as does equitable housing and job opportunities, so that these communities are brought out of poverty. 

Because the gut microbiome is deeply coevolved with the human diet, it is clear that the transition to unhealthy and degrading habits regarding the production and consumption of food is damaging to the sensitive and complex microbial system that relies on a healthy variety of plants. Each individual plant contains a unique multitude of fibers, phytochemicals, minerals and vitamins, and this diversity feeds the diversity of the microbiome. Dr. Bulsiewicz says “there are 300,000 edible plants on the planet, but 75% of our diet comes from three of them.” 

Our sterile food systems narrow down the biodiversity of our microbiome. The key is the diversification of diet: to eat as many different types of plants as possible. Currently, 97% of Americans are not getting the minimum amount of fiber and not eating enough plants. The average American diet consists of 10% plants, 560% processed food and 30% animal products. This ratio needs to change so that plants are a much bigger portion of the diet, and so that processed foods, stripped of essential nutrients, are replaced by natural foods. 

Because the gut microbiome is deeply coevolved with the human diet, it is clear that the transition to unhealthy and degrading habits regarding the production and consumption of food is damaging to the sensitive and complex microbial system that relies on a healthy variety of plants.

The good thing is that our gut can change in less than 24 hours. It is a very resilient system that operates similarly to a muscle. The key to increasing gut health is to start slowly integrating more plants into your body, and your gut will adapt, proliferating with microbes that benefit from those different types of plants. 

Changing one’s diet is a process however, and it is not always possible for people to make decisions to diversify their diet on an individual basis. Health hinges on equity, and systematic changes are necessary to provide the microcosmic gut microbiome with what it needs. 

Contact Aliya Haas Blinman at [email protected]