An Introduction to the Microbiome

Updated: Dec 7, 2021

The microbiome consists of trillions of microorganisms that work symbiotically in our bodies. This includes not just bacteria but also other organisms like fungi, parasites, and even viruses. While they exist throughout our body, they are mainly found in the stomach and the large and small intestines.


How did the microbiome come about?


Since life's beginnings, symbiosis has been a common theme among all life. Dating around 1.45 billion years ago, it is typically believed that cellular organelles such as chloroplasts and mitochondria (vital cell parts when it comes to metabolizing and storing energy) were bacteria themselves before being engulfed by the host cell and becoming integrated as part of the cell itself, as a process known as endosymbiosis.


Symbiotic relationships exist as well between more complex animals and microbes. In the Jurassic period, the extinction of large herbivorous dinosaurs allowed small mammals at the time to fill an ecological niche left behind. These mammals may have been given access to a greater variety of plant sources for food. As a result of this, their guts evolved over time to be longer and larger, with their gut microbiota changing as well, becoming more diverse. This change allowed them to break down complex sugars and other materials that would have been harder for them to break down before. Now, over 80% of all mammals are herbivorous.


Herbivory is considered one of the most important factors in determining what our microbiome will consist of. Other factors contributing to a diverse microbiome include our genome, the birth environment, the environment throughout our lifecycle, and the microbes present in breastmilk or in enhanced formulas. Because of these factors, very distinct microbiomes have evolved, in nature historically, but also within an anthropogenic environment. Humans that consume junk food, for instance, may have a significantly different microbiome compared to someone who eats a healthy omnivorous or plant-based diet.


Do we need a healthy microbiome?



The human microbiome helps to maintain a healthy state. The gut microbiome aids in digestion. Microbes break down more complex carbohydrates to form simple sugars and short-chain fatty acids, which the body is more readily able to process. These microbes produce Vitamin K2 and various B-vitamins such as B-12, riboflavin, and thiamine.


Microbes in the human gut even include bacteria normally associated with diseases such as Staphylococcus aureus, E. Coli, and Salmonella. However, it is important to understand that, though present, these bacteria may not compromise health unless the gut is compromised in some way: such as a lack of species diversity. Competition between microbial species helps to prevent any single microbe to overpopulate and cause havoc in your system.


Chronic imbalance in the gut microbiome is referred to as being in a dysbiotic state. Dysbiosis can lead to disorders and diseases such as ulcerative colitis, Irritable Bowel Syndrome (IBS), Crohn’s disease, and antibiotic-associated diarrhea. It is also believed that diseases such as diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, and fibromyalgia are connected with the microbiome as well, some of which may be passed down from parents to the child.


Gut health not only impacts bodily homeostasis but can also be influenced by and cause psychological issues. This is possible via the gut-brain connection.


What is the gut-brain connection?


The gut-brain connection is the understanding that one's mental state can be impacted by their gut and conversely, that one's gut can impact one's mental state. It has been known, for instance, that organisms can respond metabolically to perceived stimulation. For instance, just the thought of food can cause one's stomach to release juices to begin to break down food. However, we have since learned that the gut microbiota can release chemical metabolites which may influence your mood and dietary decisions. The vagus nerve is the likely culprit as it carries chemical signals from the gut to the brain. This is how your brain knows that your stomach is full. However, it sends a lot more information than that. And since the signals can go both ways, this means that your current mental health can influence your gut and vice versa. Anxiety, stress, or depression that some people feel might be related in some way to a poor gut microbiome. A poor gut microbiome may exacerbate these conditions while a healthy gut microbiome may mitigate them.


The connection between the brain and the gut is becoming more well-known. For instance,

According to Harvard Health, people who suffer from functional GI issues often feel pain more sharply than the average person. Stress or anxiety can make this pain even worse. It is also well-known that high-stress levels can result in heartburn, abdominal cramps, loose stools, and even stomach ulcers.


What supplements and methods can be used to correct the microbiome if something goes wrong?


Many people consume probiotics in the form of pills, but there isn't much evidence that doing so works for most people. This is often because for most people who are not very young or very old, adding extra bacteria to the gut does not do much to change the microbiome because it is already healthy and stable. Additionally, many capsules break down too quickly before they can reach the small intestine; therefore, bacteria may be negatively impacted by stomach acids.


Improving gut health is not a very easy task once dysbiosis has occurred, especially in Western society. One of the most important things to help is to ingest more healthy foods. Some studies show that short-chain fatty acids are thought to be very helpful in treating issues such as ulcerative colitis, IBS, Crohn’s disease, and antibiotic-associated diarrhea.


This means adding more fruits, beans, legumes, vegetables, and whole grains such as wheat and oats. These different foods include prebiotic fibers such as inulin, resistant starches, and pectins which feed the bacteria in our gut. The prebiotic fibers are then broken down into short-chain fatty acids. A fiber-rich diet is often preferred over one that is low in fiber, as less fiber generally puts you at more risk of bacteria that thrive in lower-acid environments taking over.


It is important to note that when consuming more fiber-rich foods, you incorporate them into your diet slowly. Adding too much fiber, too quickly, can result in gas and loose stools.


Adding probiotic enriched foods, such as kimchi, miso, tempeh, kombucha, and yogurt, into your diet can also help a little if you need more microbiome diversity. This helps during and after the use of antibiotics, which often kill much of the beneficial gut microbiome.


Visit this friendly video that presents many of the concepts we discussed. Enjoy.


Thank you for reading!


91 views0 comments

Recent Posts

See All