Gut Health 101: Gut Bacteria, the Gut Microbiota, and your Health

Gut Health 101: Gut Bacteria, the Gut Microbiota, and your Health

gut microbiome

A few decades ago, most health recommendations were characterized by a general “germ phobia.” We knew that specific pathogens caused severe disease, so the obvious response was to combat those germs by every means possible. What followed was the complete sterilization of our lives, a collective overdose of antibiotics that has led to severe antimicrobial resistance, and a focus on hygiene that tried to mimic the sterile conditions of a surgery ward. Fast forward a couple of decades, and we are suddenly beginning to realize that children raised in farm environments, where those dirty little microbes abound, have fewer allergies, better gut health, more robust immune systems, and are generally healthier than those children raised in the hygienic bubble we have attempted to create.  After waging war on microbes, germs, bacteria, and virtually every other invisible “threat,” we are now beginning to learn that this vastly diverse collection of microbial life plays a fundamental role in keeping us healthy. The human microbiome is the massive amount of diverse microbial life that lives on and in the human body. Though the human skin microbiome also plays a vital role as the “first line of defense” against any external pathogen that comes into contact with our bodies, this article will focus on the enormous diversity of gut bacteria and the role of gut microbiota in human health.


What is the gut microbiome?

When taking a walk through an old-growth forest, you are probably amazed by the diversity of the plant and animal life that you witness. From hundreds of different flowering plants to the mysterious buzzing insects that you have never seen, the visible biological diversity of a healthy forest ecosystem is indeed astounding. However, diversity explosion occurs when you direct your gaze to the dirt underneath your feet.

If you were to take just one spoonful of fertile soil from the floor of an old-growth forest and put it on under a microscope, you would find millions of microorganisms swarming about everywhere you look. Where our eyes see a bit of dirt, a few white strands of mycelium, and maybe a few insects, the invisible microbial world is teeming with life. Bacteria, fungi, protozoa, nematodes, and hundreds of other creatures interact in complex relationships that recycle fertility and allow the forest ecosystem to thrive.

When that complex ecosystem of microbial soil life is disturbed, the more visible aspects of the forest ecosystem (trees, birds, insects, etc.) inevitably begin to suffer. In a masterful study on the complex interactions of fungi, bacteria, tree roots, and other microbial members of the soil ecosystem, Suzanne Simard showed how the disruption of the soil ecosystem essentially made it impossible for logging companies to re-plant the forests that they had harvested.

But what does this do with the human gut and your health? Just like the soil of an old-growth forest, the human gut is also teeming with invisible microbial life. The human gut microbiome is composed of all the microorganisms, including bacteria, viruses, fungi, parasites, and other microorganisms that live in our guts. According to some estimates, there may be up to ten times more microorganisms living in and on our bodies as there are human cells. Though the human microbiome contains viruses, protozoa, and fungi, bacteria are the most numerous members of the human microbiome. Some researchers estimate that the bacterial population of the human microbiome is between 75 trillion and 200 trillion individual organisms.

Only in recent decades have researchers begun to understand how the gut microbiome works together and supports the human immune system. There are at least 1,050 different species of microbes living in your gut, and we are continuing to discover how our body and the microbe ecosystem are co-dependent on each other for health, well-being, and life itself. Just as the billions of soil microorganisms play a fundamental role in maintaining the health, resilience, and homeostasis of the old-growth forest, we are continuing to find new ways in which the microbes in our gut support our overall health. We do know that some of the microbial life in our gut produce essential vitamins and other important nutrients from the “raw” materials we provide. We also are discovering the unique ways in which the gut microbiome “programs” our immune system, metabolism, and other critical bodily functions.

However, the microbes in our gut are not simply altruistic little “helpers” but also depend on us for their survival in the same way that the soil microorganisms in the forest rely on trees and other larger flora for their existence. The microbial life in our guts relies on us for their food and for a habitable environment that allows them to thrive. Given this synergistic relationship and the unfathomable quantity of microbial life living in our guts and bodies, some researchers have begun to refer to the human-microbe ecosystem as a completely interdependent “superorganism.”


How the Gut Microbiome Affects your Health

It is important to note that we are only just now beginning to scratch the surface of the multiple ways the gut microbiome affects our health. The U.S. National Institutes of Health-sponsored Human Microbiome Project (HMP) was only launched in 2007, while the European Commission-supported Metagenomics Project of the Human Intestinal Tract (MetaHIT) was launched five years later in 2012. The fact that there is around 100 times more microbe DNA than human DNA in your body only shows that we have decades of research ahead of us to only begin to understand the countless interactions that occur inside the human gut.

Furthermore, it is worth stating that no two people will have the same gut microbiome makeup. Every individual will have a unique collection of microbiota that will thus influence and affect how our guts respond to certain foods, pathogens, diseases, etc. Though people who share an environment (such as a family) may have similar gut microbiomes, researchers believe that the gut microbiomes from one culture to the next differ on an incredible scale. In practice, this means that a “healthy” microbiome for one group or culture of people may be fundamentally different for people in a different culture who grew up eating different types of food and existing in a different type of environment.

In a recent interview with The Paleo Foundation, Dr. Momo Vuyisich stated:

Research into the role of the gut microbiome is revealing that there is no food item that is going to be healthy for everyone, and any food can be extremely health-enhancing for some people, and poison for someone else. Given this reality, a new paradigm in health and nutrition is on the horizon; one that is highly personalized and data-driven, meaning that every person will be consuming a different diet given their unique gut microbiome. The benefit of any diet will be very much determined by the microbiome of that person, which means that the same food given to two different people may have an opposite effect.

To continue with our forest metaphor, some forest fungi have evolved over millions of years to create synergistic relationships with certain species of trees. For example, whereas one species of fungi may be specially adapted to provide the birch tree with nutrients that the tree´s root systems might not be able to access otherwise, that same fungi may be pathogenic to the pine tree.

Despite the fact that every individual´s gut microbiome is different and distinctive and that these differences will lead to different health outcomes, there are a few generalized ways in which the gut microbiome can positively affect your health.

Nutrient Production: Our body requires an enormous amount of nutrients and cannot effectively obtain them from the foods we eat, even if we practice a healthy, diverse diet. The gut microbiome is the part of the body that is able to produce those nutrients for us. The gut microbiome doesn’t only play an essential role in breaking down or assimilating nutrients from food, but the microbiome also produces a significant number of critical nutrients that we cannot get effectively from food.

Control of Digestion: The microbial life in your gut is known to play a major role in helping with digestion. Specifically, researchers are discovering how gut bacteria help with carbohydrate fermentation. One study states that:

Carbohydrate fermentation is a core activity of the human gut microbiota, driving the energy and carbon economy of the colon. Dominant and prevalent species of gut bacteria, including SCFA-producers, appear to play a critical role in the initial degradation of complex plant-derived polysaccharides,11 collaborating with species specialized in oligosaccharide fermentation (eg, bifidobacteria), to liberate SCFAs and gases which are also used as carbon and energy sources by other more specialized bacteria (eg, reductive acetogens, sulfate-reducing bacteria, and methanogens).The efficient conversion of complex indigestible dietary carbohydrates into SCFA serves microbial cross-feeding communities and the host, with 10% of our daily energy requirements coming from colonic fermentation. Butyrate and propionate can regulate intestinal physiology and immune function, while acetate is a substrate for lipogenesis and gluconeogenesis.

Strengthen the Immune System: The gut microbiota also plays a fundamental role in strengthening and programming the immune system. It is estimated that around 75-80 percent of our immune system is located in our gut. Thus, a healthy gut microbiome is foundational for treating inflammation in other body parts. Some of the metabolites mentioned in the study above have been shown to play a key role in regulating immune function in the periphery, directing appropriate immune response, oral tolerance, and resolution of inflammation, and also for regulating the inflammatory output of adipose tissue, a major inflammatory organ in obesity.

Gut-Brain Axis: The gut microbiome controls virtually every aspect of our body´s functionality.  According to a recent Paleo Foundation Interview with Dr. Kiran Krishnan, he states that “there is the gut-brain access, the gut-skin access, the gut-immune axis, the gut-liver access—all of these accesses are indicative that the microbiome plays an influential role on basically every organ system in the body.” The gut-brain axis has received perhaps the most attention in recent years, and researchers are continuing to discover how a healthy gut microbiome affects our mood, our energy levels, brain wave functions, our stress response, etc.


The Dangers of Dysbiosis

Beyond these specific ways in which our gut microbiome positively affects our health, we are also beginning to discover how imbalances of unhealthy and healthy microbes in our gut may be a primary contributor to several negative health outcomes, including unwanted weight gain, obesity, high blood sugar, high cholesterol and others of the most prevalent chronic diseases affecting society.

Dysbiosis is a general term that characterizes a sub-ideal gut microbiome ecosystem. When our gut microbiome is not flourishing in quantity and diversity, the resulting dysbiosis has been shown to trigger our immune system and lead to inflammation in the body. As is well known, inflammation is the main contributor to many diseases.

Though there are several ways in which unhealthy lifestyles can negatively affect your gut microbiome, unhealthy diets, an abundance of highly processed foods, high-stress levels, frequent antibiotic use, exposure to agro-chemicals, excessive alcohol and intoxicant use, and a lack of exercise can all allow the growth of undesirable levels of microbes.

According to one recent study, “in pathological situations, dysbiosis (i.e., imbalance in gut microbiota composition) is observed with a loss in overall diversity. Dysbiosis associated with inflammatory bowel disease was specified with the reduction in biodiversity, the decreased representation of different taxa in the Firmicutes phylum, and increased Gammaproteobacteria.”



The diversity of the gut microbiome and the myriad functions it plays and contributes to led many medical professionals and researchers to consider it a separate, dynamic organ. As with any organ, the gut microbiome is altered by changes in the host, such as genetics and age, as well as environments, such as diet and antibiotic use.

Fortunately, several different strategies can help support a thriving, healthy, and diverse gut microbiome. What you eat is also what your gut microbes eat, so eating a diverse diet of fermented foods, high-fiber foods, and natural, un-processed foods should be a priority. A diverse and broad Paleo-type diet generally supports a healthy gut microbiome.

For people who are attempting to “recover” from a dose of antibiotics, a diet of highly processed foods, or a generally “sterile” lifestyle, re-inoculating your gut microbiota with beneficial microbes such as those found in fermented food or probiotics should also be a priority.

Furthermore, as research into the gut microbiome continues to evolve, individuals may be able to do a microbiome signature to gain a better understanding of the relationships between different microorganisms that affect the overall balance of the microbiome. For example, suppose a particular microbe is found at higher levels in one sample than another. In that case, it could indicate an imbalance in the microbial community that has implications for overall health. Furthermore, microbiome signatures can identify potentially beneficial microbes and their potential functions within the larger environment. This information can then be used to develop strategies that improve overall health and well-being by understanding the etiologies associated with specific microbiome signatures or promoting the growth of beneficial microbes.





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