During my sophomore year of high school, I began to have bouts of extreme stomach pain and started choking on my food at every meal. It got to the point where I needed the Heimlich on multiple occasions. Subsequently, I was diagnosed with the autoimmune condition, Eosinophilic Esophagitis. That is a fancy way of saying white blood cells were launching an immune response in my esophagus in response to food causing pain and inflammation. Little did I know, this was really a gut microbiome issue.
When steroids did not present themselves as a long-term solution I turned to functional medicine, which aims at treating the biogenesis of a disease. The functional medicine practitioners introduced me to the gut microbiome and how its damage, which causes leaky gut (discussed further later on), is the root of all autoimmune disease. As a result, I cut out trigger foods such as gluten and dairy and started eating a diet without any processed foods or any of the other junk we typically put in our bodies every day (red dye 40 anyone?). Like magic, my symptoms were gone, and my everyday well-being greatly improved.
The issue is that many people do not know the importance of their gut health and the role that microorganisms play in shaping who we are. Thus, my goal in writing this post is to explain the role of the gut microbiome, discuss why it is vital to our health, and how to best cultivate its health with a focus on best nutritional practices.
How to Understand the Research
To understand the implications of the gut microbiome, it is crucial to understand some limitations of scientific research. In this article, I cite exclusively from the primary literature and medical experts in the field to give the most in-depth and accurate look at how the microbiome functions. Although everything is based on a scientific study, not all studies are created equal and they often contradict each other. Moreover, the microbiome is a relatively new topic with limited research on its effects.
Thus, it is a field that is subject to constant change as articles are published on it frequently. Furthermore, the microbiome is a system that works in synergy with many parts of our bodies. Therefore, it is difficult to find all of its connections and pinpoint their exact mechanisms. With this in mind, all information in this paper is completely accurate regarding the current scientific literature with the caveat that not all studies are perfect, the human body is very complicated, and new information is constantly being released. Regardless, I hope you gain a better understanding of the trillions of bugs living inside you and from here on strive to develop a positive relationship with them.
What is the Gut Microbiome?
There are trillions of bacteria living inside of us, outnumbering our own cells ten to one. Moreover, there are 3.3 million microbial genes inside of you, dwarfing your 23,000 human genes. You are literally more microorganism than you are human. With this in mind, it is evident that a large group of bacteria living in our intestines, known as the gut microbiome, play a significant role in our daily wellbeing. Thus, it is important to discuss what it is, how it functions in the body, how to best cultivate it, and the broader implications of this system. However, there are more microbiomes than just in your gut. We have microbiomes on our skin, mouth, and nose to name a few. But since the gut microbiome is by far the largest group that will be the focus of this article.
The gut microbiome is essentially a collection of trillions of microbes consisting of thousands of different species coexisting inside one’s gut. These include more than simply bacteria but also fungi, parasites, and viruses. The main function of the gut microbiome is in the fermentation of resistant starches and dietary fiber which produce SCFAs (short-chain fatty acids), primarily acetate, propionate, and butyrate. These fatty acids have a wide range of effects. For example, one study suggests that propionate and butyrate promote intestinal gluconeogenesis (the production of glucose from noncarbohydrate molecules) which has positive effects on maintaining normal blood glucose and energy levels. Moreover, butyrate plays a key role in the immune system by lowering oxygen levels in the gut to kill off harmful microbes. Lastly, acetate has been shown to be a major regulator of appetite.
How Does the Gut Microbiome Affect Disease?
The gut microbiome, and the SCFAs it produces, play a broad, and loosely understood role in a wide variety of diseases, such as reducing obesity and diabetes. Furthermore, one study found a 33% decrease in microbiome diversity right before the onset of type 1 diabetes. Moreover, SCFAs have been shown to have a positive effect on irritable bowel syndrome, inflammatory bowel disease, cardiovascular disease, and various cancers.
Further, according to Harvard’s School of Public Health, “Microbiota stimulate the immune system, break down potentially toxic food compounds, and synthesize certain vitamins and amino acids, including the B vitamins and vitamin K". Although it is difficult to track exactly how and why these effects occur, it is evident that the gut microbiome plays a much larger role than simply helping to digest food, with many wide-ranging physiological changes resulting from these effects. Some prevalent doctors even attribute problems with the microbiome to all chronic diseases. For example, Dr. Gundry, founder of The Microbiome Project, provides “Until the human microbiome project was published, we didn’t listen to the fact that all disease begins in the gut and the importance of prevention”.
Much of this stems from the ability to keep at least a ratio of 85% good bacteria, and 15% of the bad bacteria. Your gut is a single layer of cells held together by tight junctions. When these junctions widen and become porous you get a condition called leaky gut. This allows a host of harmful antigens into your blood. This condition, dubbed leaky gut, is believed to be the underlying cause of all autoimmune conditions and is associated with ADHD, Parkinson's, and Alzheimer's.
Anecdotally, the experience of healing my leaky gut was one of the most profound changes in health that I have ever experienced. Gone were those inexplicable days of brain fog, unexplained tiredness, stomach pain, and all kinds of other symptoms.
The Microbiome and the Brain
There is so much to be discovered about the microbiome’s effect on the brain, as there are over 100 million neurons in the gut. This is the highest concentration of neurons in the body outside of the brain. Consequently, the microbiome can have a broad range of effects on mood, stress, and willpower. For example, serotonin, an antidepressant neurotransmitter, is produced primarily by the gut, postulating that the gut may be a key regulator in our mood. Moreover, initial studies on mice showed that fecal transplant caused the recipient to take on the personality traits of the donor, presumably due to the gut bacteria contained in the feces.
One large meta-analysis found significant effects on the amygdala, prefrontal cortex, and hippocampus. The amygdala is a major brain center in controlling emotion, postulating that the microbiome significantly affects emotion. Several studies have found a correlational link between microbial diversity and connectivity of the amygdala with other brain structures.
The prefrontal cortex is involved in executive brain functions such as judgment, planning, and problem-solving. When microbiomes were transferred from stressed to healthy mice researchers found a decrease in prefrontal cortex activity demonstrating a possible link between stress, the brain, and the microbiome. Studies have also shown mice treated with certain probiotics had increased activity in the prefrontal cortex.
Lastly, the hippocampus is an important brain structure in memory and the creation of spatial maps of our environment. Germ-free mice or mice who have been bred and raised without any microbes on them have shown decreased ability to generate new hippocampal neurons. On the other hand, probiotic treatment showed an increase in neurogenesis in the hippocampus.
So, what does all of this mean? Honestly, not too much right now. It is hard to figure out exactly what all of these changes functionally result in. More than anything, these results give us direction for further research. However, based on what we have now, it's a safe assumption to say that cultivating a healthy gut microbiome will have beneficial effects on brain health.
The microbiome also plays a significant role in mental health. Dr. Amen provides in his book The End of Mental Illness that when "the good bugs are deficient ... you are more likely to feel stressed, depressed, and tired" (137). As previously mentioned, there are 100 million neurons in the gut and your gut is responsible for synthesizing the neurotransmitter serotonin which is a prominent regulator in mood. With this, it is clear that the effects of the microbiome extend beyond the brain and into the mind.
How Can You Cultivate a Healthy Gut Microbiome?
Considering the unambiguous importance of our gut microbes in our overall health, both in preventing leaky gut, and promoting overall health, it is important to understand what helps cultivate good organisms and what cultivates bad organisms. The most important thing one can do to improve their gut health is eating a diet high in fiber, and prebiotic fiber.
Fiber literally feeds healthy gut microbes promoting healthy gut bacteria and an increase in SCFAs. Subsequently, these SCFAs protect the gut wall and provide the host of benefits mentioned earlier. In general, legumes, beans, fruit, and non-starchy vegetables are excellent sources of fiber. It is important to distinguish between soluble and insoluble fiber here. While insoluble fiber has benefits, when it comes to feeding your microbiome, soluble fiber is the way to go.
Moreover, eating fermented foods, such as yogurt and sauerkraut, or taking a reputable probiotic supplement, help to reform healthy gut bacteria while destroying the disease-causing bacteria. Lastly, eating food rich in polyphenols, such as green tea, red wine, and olive oil, among other benefits, cultivate the growth of healthy gut microbes. However, Dr. Amen also provides that unnecessary use of antibiotics, stress, sugar, artificial sweeteners, gluten, pesticides, and excessive alcohol all contribute to leaky gut syndrome and bad gut bacteria (138). Therefore, it is in one’s best interest to use antibiotics sparingly (they kill good bacteria in your gut), eat organic foods to avoid pesticides, which kill the good bugs in one’s gut, and avoid sugary or sweet food which promotes the growth of unhealthy yeasts (139-140). For more on best nutritional practices check out my last article here.
Let's talk a little bit more about probiotics. Are they actually useful? It seems like everyone is throwing bacteria into their foods so they can advertise them as containing probiotics. The main problem with taking probiotics is that they are not all the same. They all contain different strands and different amounts of the bacteria.
Usually, when you see a probiotic label on food it has added Bifidobacteria and Lactobacillus. The specifics of these two strands aren't super important but it raises the issue of why we are trying to populate ourselves with two strands when there are over 10,000 microbial species living inside of us? The answer is there is no good answer.
The research just hasn't been done so it is impossible to know which combination of microbial strands is right for each individual. Moreover, we don't even know the lasting physiological effects of probiotics, the extent to which they alter the gut, or if these changes even last. That being said, both my brother and I have gone on probiotics in the past for healing our guts, and Dr. Mark Hyman also recommends them for this purpose. I used these because they are from a very reputable source, contain 25 billion live cultures, and have all of the well-researched strands. However, these will not magically fix your gut. It is important to see their limitations and take them with plenty of fiber.
Conclusion
Given the current research on the gut microbiome, there is still a vast amount to learn.
Regardless, whether it is the obesity and diabetes epidemic, the pervasive mental health crisis, preventing cancer, or just trying to improve general wellbeing, there is a clear link to the trillions of bugs living inside of us. I firmly believe that healing all sickness starts with the gut and I strongly encourage you to focus on your gut health and see what benefits you get from it.
It's important to take small actionable steps from everything you learn. So here are some actions you can take today to have a healthier microbiome:
- Eat whole, organic, unprocessed foods
- Focus on high fiber foods like asparagus, olives, or any leafy green
- Limit sugar intake
Start these three things today and you will notice immense changes in your health!