First, consider what the “gut” is in itself. It’s helpful to consider the gut, or gastrointestinal tract, as a hose that runs through our body and is open on either end. These openings along with the continuous gut tract make the gut external to our body. So just like our skin is exposed to the outside world and all of its microorganisms, so is the inside of our GI tract (GIT). The lining that transitions from the skin to the mouth and eventually into the gut is called epithelial cells. On top of the epithelium is where the biome lives. Through simple exposure via opening our mouths, foods, drinks, breathing, etc. there is an accumulation of microorganisms that line the gut to create our gut microbiome. The collection of microorganisms, including bacteria, viruses, fungi, and other microbes, reside in the GIT, primarily in the large intestine. It is a very diverse ecosystem that plays a large role in our health. 

The microbiome impacts our immune system, nutrient absorption, production of vitamins, short chain fatty acid production, brain health, and even regulates metabolism and weight. The biome helps to defend against pathogens and reduce the risk of autoimmune conditions, allergies, and more. The biome helps to protect against pathogens by competing with harmful bacteria for resources and colonization sites as well as stimulating the production of mucus as a first line of defense. Alterations in the gut microbiome have been linked to chronic inflammation and the development of digestive disorders including irritable bowel syndrome and inflammatory bowel disease. Thus, it is important to maintain a diverse microbiome in order to promote a healthy immune system and reduce inflammation. 

Additionally, some gut bacteria produce essential vitamins, such as vitamin K and B vitamins, which are necessary for certain physiological functions. Similarly, butyrate, a short-chain fatty acid, is produced by beneficial bacteria in the gut through the fermentation of dietary fiber. It is a major contributor to the overall health of the gut by improving gut integrity, reducing inflammation, providing energy to colonocytes, promoting cell differentiation, apoptosis, potentially reducing risk for colorectal cancer. These beneficial bacteria contribute to the body’s nutrient resources and, therefore, help maintain overall health. Furthermore, the gut and brain are connected through bidirectional communication via the gut-brain axis. The microbiome contributes to brain function, mood, and behavior. Thus, imbalances in bacteria can lead to mood disorders such as anxiety, depression, and neurodegenerative disorders. Lastly, imbalances in the microbiome have been associated with metabolic diseases like obesity. Some research has shown associations with specific forms of bacteria and their impact on appetite and fat storage. Ultimately, restoring a healthy gut microbiome through interventions like probiotics or dietary changes can help alleviate symptoms, prevent disease, and support general physiological and cellular health. 

In an ideal world, there is an optimal composition between the trillions of microorganisms. The majority are bacteria, predominantly Firmicutes and Bacteroidetes. It can be difficult to maintain proper balance of this microbiome ecosystem. For instance, even a short course of antibiotics can wipe out both good and bad bacteria. If any one form of microbe has the opportunity to grow, it will (especially if given the fuel to do so) which can cause many different symptoms. Other major contributing factors that may contribute to or disrupt the microbiome include diet, stress, genetics, and environmental factors. Overgrowth and undergrowth of certain bacteria can contribute to diseases such as diabetes and prostate cancer. Finding an “optimal” composition of microbes in the gut is difficult with today’s modern stressors, but following a high-fiber and nutrient-dense diet, supplementing with gut restoring vitamins and minerals, such as magnesium or tributyrin, and reducing inflammation with things like peptides can help support a healthy gut… and a healthy human. 

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Published July 12, 2023

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