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Are You in Touch With Your Microbiome?

The relationship between the brain and gut is bi-directional.

Gut health refers to the health and functioning of the gastrointestinal tract, which extends from the mouth through to the stomach and intestines and concludes at the anus. A key aspect of gut health is the microbiome, which refers to the composition of the trillions of bacteria and other microorganisms that live within the gastrointestinal tract. In addition to facilitating the digestion and processing of food, the gut microbiome plays an important role in helping the body maintain a state of equilibrium and wellbeing.

Being able to break down and absorb nutrients efficiently is obviously important for providing the body with energy and fostering healthy cell growth and repair. However, the gut microbiome is also linked to various aspects of bodily and psychological functioning, ranging from the operation of the immune system and how we regulate stress to the presence of conditions such as diabetes, heart problems, depression, and anxiety. Some more obvious examples of health issues linked to the microbiome include bloating, gas, diarrhea, nausea, and inflammation of the intestinal lining.

Dysbiosis is a term used to describe an imbalance in the microbiome, which can lead to an overgrowth of opportunistic gastrointestinal microorganisms, a reduction in the production of short-chain fatty acids, and reduced resistance to intestinal pathogens. The depletion of beneficial bacteria that occurs during dysbiosis is also understood to impair the immune system and trigger inflammatory disorders such as inflammatory bowel disease.

The Gut-Brain Axis

Communication between the brain and gut occurs via the gut-brain axis and is understood to reflect a complex bi-direction relationship. This means that a reduction in our psychological health can disrupt information flow via the gut-brain axis and impact our gut health. The same applies in the other direction, such that if our gut health becomes compromised, it can have a knock-on effect on brain functioning and mental health. The relationship between the gut and brain is supported by brain imaging studies, where (for example) ingesting fermented milk containing probiotic bacteria has been shown to prompt alterations in brain activity that are different from individuals who ingest unfermented milk without probiotic bacteria.

Microbiome and Mental Health

A healthy balanced diet is obviously important for maintaining optimum gut health, as are general wellbeing principles such as taking regular exercise and maintaining good sleep hygiene. However, of equal importance is taking care of our mental health because given the bi-directional nature of the gut-brain relationship, if we are feeling stressed or worn down it will likely cause imbalance and stress to our microbiome.

According to Dr. Househam and colleagues in a paper published in Advances in Mind-Body Medicine, psychological stress can induce a fight-or-flight response that triggers the release of chemicals such as corticotropin-releasing hormone and catecholamine, which have a negative impact on gut bacteria. Conversely, keeping psychological stress under control allows beneficial bacteria and microorganisms to produce short-chain fatty acids that have anti-inflammatory and anti-tumor effects.

Me and My Microbiome

It’s not quite accurate to think of the body as being distinct from the various bacteria and microorganisms that live within it. This is because to a large extent, such microbiota are a core component of the body. Indeed, beneficial gut microbiota not only play a key role in keeping us healthy, but are essential for our survival.

Therefore, when we refer to “me,” “I,” or “self,” this includes the trillions of bacteria and microorganisms that live in the gut and elsewhere in the body. For some people, it might feel strange to think of themselves as a composite including trillions of bacteria and microorganisms, but relating to the “self” in this manner is in line with increasing psychological and scientific efforts to foster a better understanding of exactly what constitutes the “self.” This is particularly the case within my own field of contemplative psychology, where as discussed in a previous post, the “self” is increasingly being conceptualized as a more encompassing, unfixed, and interconnected entity.


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Dubois T, Reynaert C, Jacques D, Lepiece B, Zdanowicz N. (2019). Role of gut microbiota in the interaction between immunity and psychiatry: a literature review. Psychiatria-Danubina, 31(Suppl 3), 381-385.

Househam AM, Peterson CT, Mills PJ, Chopra D. (2017). The Effects of Stress and Meditation on the Immune System, Human Microbiota, and Epigenetics. Advances in Mind Body Medicine, 31, 10-25.

Kaplan, B. J., Rucklidge, J. J., Romijn, A., & McLeod, K. (2015). The Emerging Field of Nutritional Mental Health: Inflammation, the Microbiome, Oxidative Stress, and Mitochondrial Function. Clinical Psychological Science, 3(6), 964–980.

Maes, M., Kubera, M., Leunis, J. C., Berk, M., Geffard, M., & Bosmans, E. (2013). In depression, bacterial translocation may drive inflammatory responses, oxidative and nitrosative stress (O&NS), and autoimmune responses directed against O&NS-damaged neoepitopes. Acta Psychiatrica Scandinavica, 127, 344–354.

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Tillisch, K., Labus, J., Kilpatrick, L., Jiang, Z., Stains, J., Ebrat, B.,. Mayer, E. A. (2013). Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology, 144, 1394–1401.