Microbiome and Gut Health

Would you believe it if you were told that at this very moment there are more little organisms on and in your body than there are people that live on earth? It’s a crazy thought but it’s true! The microbiome is the star of this blog post today and is gaining interest in the scientific community. 

What is the microbiome? It’s a collection of microorganisms that is primarily bacteria, cells, viruses, fungi, protozoa, and other organisms (1). There are approximately 100 trillion microbes that are primarily living within the digestive tract (1). It’s so large but seemingly invisible that it’s considered the “virtual organ”. Researchers are learning that it is intimately connected to health. It impacts your mood, the clarity of your thoughts, how you perform physically, and it impacts your immune system, and how often you get sick. The human digestive tract is like a donut. It’s open from one end (the mouth) to the colon and includes everything in-between and the microbiome is a part of that. Now you know that the microbiome is a collection of microorganisms in a specific environment. The microbiota is the actual community of organisms themselves (1). Let’s talk a little bit about diversity. The topic of diversity is forefront in today’s society. It’s important, and when there is a lack of diversity it can cause unrest and long-term damage. The same concept applies to your microbiome. Microbiota diversity is a measurement of how many different species of organisms are within the microbiome and the microbiota communities (1). The less diverse the microbiome the more dysbiosis (microbial imbalance) occurs within the gut, which researchers are linking to obesity, cardiometabolic conditions, autoimmune conditions, diabetes, emotional conditions, and cognitive decline in the elderly (1). The microbiome has many functions but some of the main ones include assisting with digestion, nutrient absorption, and immune response (2). Factors that impact the microbiome include but are not limited to diet, stress, environmental exposures, physical activity, sunlight exposure, medications, infections, and pregnancy exposure (2). 

How healthy and diverse the gut microbiome is impacts how well nutrients are absorbed from the food you eat. It helps synthesize vitamins, acts as a barrier against pathogens, helps in the production of short-chain fatty acids, how well you sleep, and aids in the renewal of cells within the gut (3,4). It makes sense then, that nutrition matters. What you eat impacts your microbiome just as much as the microbiome impacts how well it digests the food you consume. Eating poorly can change the composition of your gut over time and it can prevent you from absorbing the nutrients your body needs to stay healthy. All these little organisms help with the digestion and absorption of nutrients from food, so let’s take a closer look at a few molecules that our bodies need to survive and how the microbiome comes into play to assist.


The molecule tryptophan is an essential amino acid and is found in foods such as turkey, chicken, eggs, milk, cheese, and chia seeds. The body and the microbiota within the microbiome take Tryptophan and convert it into multiple important molecules (5). Two of those molecules are serotonin (happy hormone) and melatonin (sleepy hormone). If you don’t consume enough tryptophan or your body cannot properly digest it then serotonin and melatonin will be imbalanced (5). You may feel less happy with poor serotonin production and you may not be sleeping as well with the disruption of melatonin.


The compound tyrosine is an amino acid that is found in foods such as almonds, seeds, lentils, cheese, and some meats. Like tryptophan, tyrosine is converted into other compounds. Dopamine (helps with motivation) and epinephrine (flight or fight hormone) are two such compounds that tyrosine is converted into (6). Without dopamine, you may feel less motivated, tired, and lethargic. Without epinephrine, your response to situations that need a quick reaction may be lagging (6). If a vicious dog starts chasing you, epinephrine kicks in and you start running away as fast as you can. That’s good, you want that response. It might save your life.

Indole-3-Lactic Acid (ILA):

ILA is found in fermented foods such as kimchi, pickles, kefir, and sauerkraut. It is a metabolite of tryptophan (7). Gut bacteria will convert ILA into indole propionic acid (IPA), which is an antioxidant and acts as scavengers to help fight against free radicals that cause damage to your cells (7). Over time cell damage can lead to poor health and cancer.

What you eat is necessary to stay healthy, however, it is just as necessary to have a healthy and diverse microbiome to utilize the nutrients from what you consume. To use and convert nutrients from your food into usable compounds that nourish your body the microbiome is most efficient when balanced. There are trillions of these organisms that have very specific jobs and that is why diversity is so important. Your gut is smart, it learns what you eat in the long run. If you have a diet that primarily consists of highly processed and fatty foods, your microbiome will adapt to respond to those foods by overcompensating and making more bacteria that are only specific to that diet. This may lead to an imbalance of bacteria over time. The microbiome has a significant impact on nutritional status, health, and well-being. How much of an impact it has is still being discovered and more research is needed to fully understand this complex relationship between the microbiome and health. Given what we do know, it is important to nourish our bodies with a well-balanced diet that promotes diversity within our digestive system to promote healthy immune systems, better sleep, and improved emotional and mental health.




  1. https://www.bmj.com/content/361/bmj.k2179
  2. Martin FP, Dumas ME, Wang Y, et al. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol. 2007;3:112. doi:10.1038/msb4100153
  3. Pull SL, Doherty JM, Mills JC, Gordon JI, Stappenbeck TS. Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. Proc Natl Acad Sci U S A. 2005;102(1):99-104. doi:10.1073/pnas.0405979102
  4. O’Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep. 2006;7(7):688-693. doi:10.1038/sj.embor.7400731
  5. Kaur H, Bose C, Mande SS. Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis. Front Neurosci. 2019;13:1365. Published 2019 Dec 18. doi:10.3389/fnins.2019.01365.
  6. Oliphant K, Allen-Vercoe E. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome. 2019;7(1):91. Published 2019 Jun 13. doi:10.1186/s40168-019-0704-8
  7. Wong CB, Tanaka A, Kuhara T, Xiao JZ. Potential Effects of Indole-3-Lactic Acid, a Metabolite of Human Bifidobacteria, on NGF-induced Neurite Outgrowth in PC12 Cells. Microorganisms. 2020;8(3):398. Published 2020 Mar 12. doi:10.3390/microorganisms8030398

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