For decades, we did not fully understand the functional purposes of many parts of the human body. The spleen was once thought of as dispensable, earwax merely as dirty waste and the appendix as a useless leftover from the course of human evolution. But science has a habit of humbling us and we now know that all of these components serve essential purposes in the human body. Our understanding of the gut microbiome is following a similar pattern. However, beyond knowing that it plays a role, we still lack a full understanding of the true nature and mechanisms of this mysterious system.

Given the average person's current understanding of microbes, it is unsurprising that they are often associated with disease, capable of causing some of the most deadly disorders. They are thought of as a foreign figure entirely and that should remain separate from us. Nevertheless, just like their occupation all over our skin, our gut is home to them too.

When we think of our own identities, we tend to boil ourselves down to a singular body, a singular self. Typically, we define ourselves by our jobs, the activities we enjoy and the values we admire - elements all tied to a single individual. Yet, within us lives an entire biosphere that hosts a whole community of microbes. These minute beings govern our guts in symbiosis with other systems of the human body and outnumber human cells ten to one (1). It is a wonder how we are home to trillions of bacteria and are barely conscious of their existence. How do these seemingly fatal organisms operate cooperatively with the body? Can we construe the self as a singular individual when our body is a complex community with seemingly precarious organisms living within us?

“What lies behind us and what lies before us are tiny matters compared to what lies within us” - Ralph Waldo Emerson

The community that is composed of bacteria, fungi, viruses and archaea plays a significant role in many aspects of our lives, affecting the way we digest food down to the regulation of our mental health. 

We understand the digestive system to be composed of the mouth, stomach, intestines and other vital organs as the main drivers of digestion. Similarly, the immune system depends on the bone marrow, spleen, white blood cells and antibodies to suppress an infection. Yet, the microbes sequestered within our gut assist extensively in driving the actions associated with these systems. In digestion, the range of their skill extends from the ability to synthesise vitamin K to using cross-feeding mechanisms - a phenomena where one bacterium breaks down parts of plant compounds and passes the byproducts to others, resulting in boosted health (2,3). They have also been shown to promote gut barrier integrity to prevent the entry of harmful pathogens, while also aiding in regulating immune system homeostasis, assisting the body in blocking harmful pathogens and enabling a strengthened immune response in the face of infection (3).

Although there has been extensive research conducted to investigate the role of gut microbes in our physical health, their effects on our mental health have often been overlooked. Yet, they play a fundamental role in its regulation and the promotion of positive wellbeing. This contribution is most evident in the context of the gut-brain axis, which consists of two-way signalling between the central nervous system and enteric nervous system, serving the emotional and cognitive domains of the brain. Working hand-in-hand, the mental state of an individual can cause harmful alterations to the composition of healthy gut microbes and in a reciprocal manner, a dysregulated gut flora can adversely affect the brain through pathways such as immune activation and the production of neuroactive substances (4). Such imbalances in the gut microbiota have been linked to the emergence of depressive-like behaviours (5), though there is an increased prevalence of other psychiatric disorders like bipolar disorder, schizophrenia and anxiety that occur as a result too (6). 

The last decade of science has demonstrated a dramatic increase in the understanding of the gut microbiome as we know it today. Like in any field however, there is still more to be discovered. Similar to the infamous genome-wide association studies that assist in the recognition of certain genetic markers to particular diseases or traits through a statistical basis, metagenome-wide association studies are being conducted to identify associations with microbiome structures and several major diseases (7). Research in this field has already allowed for the detection of shifts in gut compositions and how these changes functionally contribute to many metabolic diseases. However, small sample sizes for such research highlight the requirement for greater development within the field. 

“The self is not something ready-made, but something in continuous formation through choice of action” - John Dewey

The human body has a mutual relationship with the gut microbiome, like that of the gut-brain axis. So when one of these systems is not functioning at its peak, the performance of the other is also derailed. Dysbiosis of the gut's natural flora contributes to clinical conditions such as Irritable Bowel Syndrome (IBS), Autism Spectrum Disorder (ASD) and anxiety (4). However, microbial imbalance is mediated through the actions and behaviours of the individual at hand. Both chronic and acute stressors can increase gut barrier permeability, resulting in a “leaky” gut, allowing bacteria to seep into the cracks and trigger an array of physiological responses like inflammation.  

It is safe to say that there is no single, definitive state that our individual guts exist in. In a world driven by antimicrobial usage, fluctuating diets and the invisible weight of daily stress, the gut microbiome remains in a state of constant transformation. Ever-changing, they mirror the conscious and unconscious choices we make, ultimately shaping our health in ways we are only beginning to imagine.

References

1. National Institutes of Health (NIH) [Internet]. 2015 [cited 2025 Jun 1]. NIH Human Microbiome Project defines normal bacterial makeup of the body. Available from: https://www.nih.gov/news-events/news-releases/nih-human-microbiome-project-defines-normal-bacterial-makeup-body

2. Mueller C, Macpherson AJ. Layers of mutualism with commensal bacteria protect us from intestinal inflammation. 2006 Feb 1 [cited 2025 Jun 1]; Available from: https://gut.bmj.com/content/55/2/276

3. Zhang YJ, Li S, Gan RY, Zhou T, Xu DP, Li HB. Impacts of Gut Bacteria on Human Health and Diseases. International Journal of Molecular Sciences. 2015 Apr;16(4):7493–519.

4. Carabotti M, Scirocco A, Maselli MA, Severi C. The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Ann Gastroenterol. 2015;28(2):203–9.

5. Bested AC, Logan AC, Selhub EM. Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: Part I – autointoxication revisited. Gut Pathogens. 2013 Mar 18;5(1):5.

6. Nikolova VL, Smith MRB, Hall LJ, Cleare AJ, Stone JM, Young AH. Perturbations in Gut Microbiota Composition in Psychiatric Disorders: A Review and Meta-analysis. JAMA Psychiatry. 2021 Dec 1;78(12):1343–54.

7. Wang J, Jia H. Metagenome-wide association studies: fine-mining the microbiome. Nat Rev Microbiol. 2016 Aug;14(8):508–22.