The Gut Microbiome

  The microbiome is a very new and exciting field. We’re just starting to understand the effect of the gut on the rest of the body. Our actions affect our microbiome, and our microbiome affects our thoughts and feelings. Let’s get into just what our microbiome is, how it works, and what we can do to support our brain health via caring for our unique macrobiotic makeup.

First, what is the human gut microbiome? The human microbiome refers to the vast and diverse community of microorganisms that inhabit the human body. These microorganisms include bacteria, viruses, fungi, and other single-celled organisms. The majority of the human microbiome is composed of bacteria, with an estimated 100 trillion bacterial cells, outnumbering human cells by approximately tenfold. These microorganisms reside in various parts of the human body, with the gut being the most densely populated. Other significant microbiome-rich areas include the skin, oral cavity, respiratory tract, and reproductive organs. Each region of the body has a unique microbial composition, influenced by factors such as genetics, diet, environment, and lifestyle. The human microbiome plays a crucial role in maintaining overall health and well-being.

Here's how it works: the relationship between the human host and its microbiome is one of mutualism and symbiosis. This means that both the host and the microbes benefit from this relationship. The host, AKA us, provides a suitable environment and nutrients for the microorganisms, and in return, the microbiome aids in various physiological processes. Firstly, the gut microbiome plays a vital role in the breakdown and absorption of nutrients from food. Certain microorganisms help digest complex carbohydrates, fibers, and other substances that human enzymes cannot process on their own. In this process, they produce short-chain fatty acids and other metabolites, which can positively influence our health. This is why fiber is an important part of diet, as fiber primarily benefits the “good” microflora.

The microbiome also helps in training and modulating the immune system. By interacting with immune cells, it aids in the development of a robust immune response while preventing unnecessary inflammation or autoimmunity. The microbiome creates a protective barrier by occupying niches on the body's surfaces. This competitive exclusion prevents the colonization of harmful pathogens and helps maintain a healthy microbial balance, preventing infections. As well as protecting us, some microorganisms in the microbiome can produce vitamins, such as B vitamins and vitamin K, which are essential for our health.

As well as these known benefits, emerging research suggests that the composition of the gut microbiome may influence energy balance and metabolism, affecting factors such as weight management. There is evidence of bidirectional communication between the gut and the brain, known as the brain-gut axis. The microbiome is believed to influence brain function and behavior through various signaling pathways. Disruptions or imbalances in the human microbiome, known as dysbiosis, have been associated with several health conditions, including gastrointestinal disorders, allergies, autoimmune diseases, obesity, and even mental health issues. In the words of Andrew Huberman, “Our body is shaping the decisions that our brain is making and we’re not aware of it, at all.”

Microbiota changes your brain by metabolizing or facilitating the metabolism of neurotransmitters. In this way, certain microbiota can improve or diminish your mood: microbiota are converted into various neurochemicals such as gaba, and influence the way your brain functions. Our experience with certain foods involves tastes, textures, and subconscious processing of taste in our gut that signals certain neuromodulators via the microbiota. Essentially, the gut communicates to the brain to change what we think we want or to change our actual behaviors around food. 

So, we can create the correct environment for microbiota to thrive, and therefore enhance our mood and behavior. Let’s first discuss the architecture of the digestive tract to understand how we can make changes before we get into actionable protocols.

The gut and the brain are bidirectional biological circuits. They are always in communication: your gut influences your brain and the brain influences your gut. Your digestive system begins at your mouth and ends at your anus, sectioned off by sphincters. Microbiotas (the good bacteria in the microbiome) live in the lumen of the digestive tract and thrive to varying degrees along the length of the path depending on the acidity and environment. You’re constantly making and secreting micro-bacteria, and their populations vary based on the choices you make. Some microbiota prefer some foods over others, but we’ll get to that later.

Behaviors and experiences alter microbiota, starting right when you’re born. When you are born without surgical intervention, the mother’s vagina has colonies of microbiota that attach to you upon birth. As such, you get a sample of your mother’s own microbiome the moment you reach the air. Birthing by C-section removes this early exposure to microbiota, which may be slightly detrimental to the infant’s immune health. Other factors including pet ownership, outside play, etc. also affect the early microbiome.

Now, how does the microbiota work? Neurons in the gut are activated when sugar, fatty acids, and amino acids are present. Nerve cells (specifically called neuropod cells) in the gut are collecting information about what’s there and sending that information up to the brain via the vagus nerve. Neuropod cells sense nutrients, particularly sugar, which activates areas of the brain that cause you to seek out more of that food. The selective preference for seeking out sweet foods occurs even if you can’t taste the food, actually! Experiments have been conducted where sugar is injected straight into the gut of participants, and they get cravings for more sugar despite never tasting any. This tells us that sugar craving isn’t simply a function of taste. We don’t just like sweet foods – we have a gut sensation below conscious detection.

The mechanism of sugar craving is primarily driven by dopamine, known fittingly as the “motivation and drive” neurotransmitter. Dopamine, when released, causes us to seek out more of the sensation of delight and satisfaction from what we eat. In addition to dopamine, ghrelin is a hormone produced to induce hunger. It increases with fasting and stimulates the feeling of hunger by inducing hormones like epinephrine, also known as adrenaline. In the other direction, the glucagon-like pathway (GLP-1) is made by neurons in the gut and brain. It inhibits feeding and reduces appetite, and can be stimulated with yerba mate tea, avocado, eggs, and the state of ketosis. GLP-1 and ghrelin are examples of gut-brain signaling mechanisms that adjust appetite and are dependent on diet.

There are indirect signaling pathways as well. The environment of the gut microbiome can create chemical substrates that allow your brain to feel one way or another. Particular gut microbiota can create dopamine in the gut, as mentioned before, which enters the bloodstream and changes baseline levels of dopamine in the brain and body. Other microbiota can create serotonin and determine levels of serotonin released during certain events, which is important for quality sleep and good mood. In fact, the majority of serotonin is manufactured in the gut and released by neuromodulators in the brain in response to touch or social experiences.

Alright, so we’ve covered dopamine, serotonin, ghrelin and opposing pathways, and other modulating factors for the gut. How can we improve our gut health with this new information?

1. The first step is before you even make food choices on your own. For parents: the more diversity you can create early, the better chance you’re giving your child of healthy brain-gut signaling and immunity. This means introducing a variety of foods to your child as soon as you can, which will also likely lessen the risk of pickiness.

2. Some have asked about fasting for gut health. Though fasting has a lot of benefits, we don’t know whether it promotes or degrades the microbiome over time. So far, prolonged fasting seems to cause disruption for microbiota, the same as food scarcity would be for larger organisms.

Non-Diet-Related Ways To Create A Healthy Gut Microbiome:

1. Get deep sleep; set consistent sleep and wake times to maximize recovery during sleeping hours.

2. Maintain proper social interactions: This improves mental health, better supporting the gut through less social stress.

3. Limit prolonged stress and stressors: the stress you experience outwardly affects your gut as well.

Diet and Nutrition

1. Fermented foods (4-6 ounces per day) increase gut biodiversity and decrease inflammatory signals and activity! Consistency over quantity for this stuff. 

• Focus on low-sugar fermented foods with live active cultures: plain yogurt (not fruit flavors) and kefir, kimchee, sauerkraut

• When starting to increase fermented food intake, increase servings over time and spread throughout the day to limit any gastric distress you may initially have

2. High-fiber diets may be useful for overall health but don’t necessarily lead to increased gut biodiversity. Though fiber doesn’t have an impact on gut biodiversity, some people experience a decrease in inflammatory markers.

3. There is evidence in animal models that ingesting artificial sweeteners such as sucralose can disrupt the gut microbiome. Take this with a grain of salt, since it’s not proven in humans, but still something to consider.

Lastly, how do you even know if your gut health is getting better? Here are a few signs:

1. Regular and pain-free bowel movements. Pooping shouldn’t be painful, basically.

2. Consistent energy. You don’t have an energy crash at any point in the day.

3. Normal amount of gas and bloating. You don’t bloat up after meals in a significant way, nor is it uncomfortable.

4. Healthy bowel transit time. You should have a bowel movement once a day, if not more.

5. Mental clarity. Poor gut health can cause brain fog and memory deficiencies.

6. Healthy reactions to food and stress. Perhaps you feel less sensitive to some foods that used to bother you, etc.

Give these tips a try if you’re interested and best of luck on your health journey.

Sources:

Buchanan, K.L., Rupprecht, L.E., Kaelberer, M.M. et al. The preference for sugar over sweetener depends on a gut sensor cell. Nat Neurosci 25, 191–200 (2022). https://doi.org/10.1038/s41593-021-00982-7

Hannah C. Wastyk, Gabriela K. Fragiadakis, Dalia Perelman, Dylan Dahan, Bryan D. Merrill, Feiqiao B. Yu, Madeline Topf, Carlos G. Gonzalez, William Van Treuren, Shuo Han, Jennifer L. Robinson, Joshua E. Elias, Erica D. Sonnenburg, Christopher D. Gardner, Justin L. Sonnenburg, Gut-microbiota-targeted diets modulate human immune status, Cell, Volume 184, Issue 16, 2021, Pages 4137-4153.e14, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2021.06.019. (https://www.sciencedirect.com/science/article/pii/S0092867421007546)

Rao, Satish S. C. MD, PhD, FRCP (LON)1; Rehman, Abdul MD1; Yu, Siegfried MD1; de Andino, Nicole Martinez ARNP1. Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis. Clinical and Translational Gastroenterology 9(6):p e162, June 2018. | DOI: 10.1038/s41424-018-0030-7 Lee, SH., Yoon, SH., Jung, Y. et al. Emotional well-being and gut microbiome profiles by enterotype. Sci Rep 10, 20736 (2020). https://doi.org/10.1038/s41598-020-77673-z

AUTHOR=Nguyen Tanya T., Zhang Xinlian, Wu Tsung-Chin, Liu Jinyuan, Le Collin, Tu Xin M., Knight Rob, Jeste Dilip V, TITLE=Association of Loneliness and Wisdom With Gut Microbial Diversity, Composition: An Exploratory Study, JOURNAL=Frontiers in Psychiatry, YEAR=2021, URL=https://www.frontiersin.org/articles/10.3389/fpsyt.2021.648475, DOI=10.3389/fpsyt.2021.648475, ISSN=1664-0640

Martina Sgritta, Sean W. Dooling, Shelly A. Buffington, Eric N. Momin, Michael B. Francis, Robert A. Britton, Mauro Costa-Mattioli, Mechanisms Underlying Microbial-Mediated Changes in Social Behavior in Mouse Models of Autism Spectrum Disorder, Neuron, Volume 101, Issue 2, 2019, Pages 246-259.e6, ISSN 0896-6273, https://doi.org/10.1016/j.neuron.2018.11.018. (https://www.sciencedirect.com/science/article/pii/S0896627318310092)

doi: 10.1146/annurev-neuro-091619-022657, URL: https://doi.org/10.1146/annurev-neuro-091619-022657