The Secret Workings of The Gut Microbiome

Known as the ‘second brain’, the gut plays many roles in the body from controlling functions like swallowing to impacting mood. A huge part of it is the gut microbiome. Thought of as a virtual organ because of its importance, the gut microbiome is a complex system of over a 100 trillion living microorganisms. These microscopic organisms can reflect not just the stomach’s health, but the health of the entire body (Feed Your Gut, 2021).

Figure 1. A diagram of the various physiological functions the gut microbiome contributes to (Afzaal et al., n.d.).

How your gut works

Every person has a unique gut microbiome populated with species of bacteria, viruses, fungi and parasites. This unique makeup is introduced during birth and infancy, then later develops and evolves as one’s diet changes over time. Most of the organisms in the gut have a symbiotic relationship with the body: the body provides shelter and food, while they complete services that the body can’t on its own. For example, the good bugs help break down certain complex carbohydrates and dietary fibers as well as various vitamins including B1, B9, B12, and K. Beneficial microorganisms also keep harmful bugs in check, produce neurotransmitters like serotonin which regulate mood, and support immune system health (What Is Your Gut Microbiome?, n.d.). A balance of these various  microbes is key for overall health—something that can be greatly improved through a  balanced diet. 

Figure 2. Foods high in fiber that gut microbes can use to support gut function (Younkin, 2025).

Importance of a balanced diet

Diet determines the exact makeup of the gut microbiome. Like all living organisms, the  microbes in the gut thrive in certain conditions. The natural acidity of the gut is the right  balance: it isn’t so acidic that all the good microorganisms die off, but it is acidic enough to kill off most bad microorganisms. Any unhealthy diet, especially the Western diet high in processed foods, red meat, and fat, can push the gut away from ideal conditions. Specific foods can also help introduce the right bacteria to the gut. Probiotics, for example, are one of the many ‘good bugs’ that improve digestion and kill off harmful bacteria. They are found in all fermented foods including yogurt, sauerkraut, and kimchi (Oliveira, 2025). Just eating some of these ‘gut friendly’ foods occasionally won’t help—these must be consistently integrated into a person’s diet. 

Key Takeaways

It is important to keep the gut microbiome healthy as it influences almost every system in the body. The best way to support a healthy gut is by paying attention to the foods you eat and aiming for balance and variety in your diet. By including fruits, vegetables, whole grains, and  fermented foods, you create the best environment for the good microbes to thrive. Taking care of your gut isn’t just about digestion, but it's a key part of long-term health, increased immunity, and even a better mood. 

References

1. Feed your gut. (2021, April 1). Harvard Health. https://www.health.harvard.edu/staying-healthy/feed-your-gut

2. Afzaal, M., Saeed, F., Shah, Y. A., Hussain, M., Rabail, R., Socol, C. T., Hassoun, A., Pateiro, M., Lorenzo, J. M., Rusu, A. V., & Aadil, R. M. (n.d.). Frontiers | Human gut microbiota in health and disease: Unveiling the relationship. Retrieved March 6, 2026, from https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.999001/full

3. What Is Your Gut Microbiome? (n.d.). Cleveland Clinic. Retrieved March 6, 2026, from https://my.clevelandclinic.org/health/body/25201-gut-microbiome

4. Oliveira, N. (2025, March 4). Probiotics for Gut Health. The Nutrition Source. https://nutritionsource.hsph.harvard.edu/probiotics/

5. Younkin, L. (2025, March 21). Best Foods to Eat for Gut Health. EatingWell. https://www.eatingwell.com/article/2059033/best-and-worst-foods-to-eat-for-gut-health/

Thumbnail Image: (Younkin, 2025)