top of page

Your gut on meditation

Updated: Jun 4, 2020

Did you know that meditation can affect your gut? It’s been shown in research to benefit individuals with irritable bowel syndrome (IBS) [1][2]. Meditation also helps you maintain a healthy-gut barrier by decreasing stress related inflammation in the body [3]. A damaged barrier can lead to leaky gut, which could allow food components, toxins and bacteria to leak into the bloodstream [4].

How To Meditate

Meditation is gaining increased popularity for diverse medical conditions [3]. What’s great about meditation is that it can be done anywhere and it’s completely FREE, unless you splurge and buy an app subscription. I’m currently using Calm but some others include Headspace, Insight timer and 10% Happier. There’s also the option of YouTube channels – I quite enjoy “The Honest Guys”.

The two challenges I see in practice and have experienced myself with following a daily meditation practice:

  1. Finding the time

  2. Believing that meditation involves having a “blank mind”

The time fallacy. If only there were more hours in a day! No matter how packed your day is with lists of things to accomplish, there’s always a few minutes that can be squeezed in for meditation whether that be on a lunch break, on first waking or before going to bed. Schedule it in your calendar so it becomes a daily habit. Your mind will thank you and in turn, it will help you become more focused, calm and resilient to daily stresses.

A big misconception about meditation is that it isn’t being done right unless the mind goes blank. Meditation doesn’t have a right or wrong. It’s a nonjudgmental process involving being in the present moment and focusing on the breath or a certain mantra. It’s only normal that thoughts come in and out but the importance is to acknowledge these and refocus. “The goal of meditation isn’t to control your thoughts, it’s to stop letting your thoughts control you.”

The Science

Gut-Brain Axis (See diagram below for a visual)

The reason for meditation’s beneficial effects are due to the gut-brain axis [5]. This is a bidirectional pathway between the central nervous system (brain and spinal cord) and the gastrointestinal tract, including both its microbiome and the enteric nervous system [6]. The enteric nervous system is sometimes referred to as our “second brain” since it can work independent of the brain and spinal cord [7]. It consists of neurons that govern the function of the gastrointestinal system including motility, blood flow, fluid transport and the handling of nutrients [8].

The central nervous system (CNS) communicates with the gut through branches of the autonomic nervous system (ANS) including the parasympathetic (rest and digest) and sympathetic (fight or flight) divisions [6]. Some stress is beneficial but when this becomes chronic, overactivation of the fight or flight system can hinder normal gut function and promote disease [10]. The accompanying immune activation in response to stress can also lead to inflammation [3]. Meditation activates the parasympathetic system, which helps with digestive disorders [9] and decreases biomarkers of inflammation [3].

The hypothalamic-pituitary-adrenal (HPA) axis is another important component of the gut-brain axis. The hypothalamus portion of the HPA axis is part of the limbic system, which plays a role in emotional responses and memory [6]. The HPA axis helps in adaptive responses to any kind of stress. Under chronic stress, the HPA axis is no longer able to adapt by decreasing inflammation associated with activation of the sympathetic system [3]. Normally under stress, corticotropin-releasing factor (CRF) from the hypothalamus in the brain gets released which causes adrenocorticotropic hormone (ACTH) to be secreted by the pituitary gland, causing cortisol release from the adrenal glands. Cortisol, the main stress hormone, can affect many organs including the brain and gut [6]. With regards to the gut, stress can affect gut permeability and alter the microbiome [3][11]. The good news is that research has shown that meditation can help regulate cortisol levels [3].

Image adapted from Reference [6] Microbes in the Gut

Let’s not forget about the trillions of microbes in the gut, which also influence the gut-brain axis [3]. Gut microbes interact with the CNS through the nervous, endocrine and immune systems. And the brain influences the composition and functions of the microbes in the gut through signals from the autonomic nervous system [12]. Some of the earliest studies on the microbiome-gut-brain axis were conducted in animals and showed that both introduction of pathogenic bacteria as well as germ free mice, can impact behavior and increase the stress response [13]. Research is still needed but it would be interesting to see if meditation has a positive impact on microbial gut composition since it is a stress reducing technique.


  1. Keefer, L. and Blanchard, E.B. 2002. A one year follow-up of relaxation response meditation as a treatment for irritable bowel syndrome. Behaviour Research and Therapy. 40: 541-546.

  2. Gaylord, S.A. et al. 2011. Mindfulness training reduces the severity of irritable bowel syndrome in women: results of a randomized controlled trial. American Journal of Gastroenterology. 106(9):1678-1688.

  3. Househam, A.M., Peterson, C.T., Mills, P.J. and Chopra, D. 2017. The Effects of Stress and Meditation on the Immune System, Human Microbiota, and Epigenetics. Advances in Mind Body Medicine. 31(4): 10-25.

  4. Camilleri, M. 2019. Leaky gut: mechanisms, measurement and clinical implications in humans. Gut. 68(8): 1516-1526.

  5. Dossett, M. 2019. Brain-gut connection explains why integrative treatments can help relieve digestive ailments. Harvard Health Publishing. Accessed from:

  6. Carabotti, M., Scirocco, A., Maselli, M.A. and Severi, C. 2015. The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Annals of Gastroenterology. 28: 203-209.

  7. Society for Neuroscience. “‘Second brain’ neurons keep colon moving: Brain in the gut coordinates activity of millions of neurons to propel waste through digestive system.” ScienceDaily. Accessed from:

  8. Furness, J.B. 2012. The enteric nervous system and neurogastroenterology. Nature Reviews Gastroenterology and Hepatology. 9(5):286-294.

  9. Breit, S., Kupferberg, A., Rogler, G. and Hasler, G. 2018. Vagus nerve as Modulator of the Brain-Gut Axis in Psychiatric and Inflammatory Disorders. Frontiers in Psychiatry. 9:44.

  10. Konturek, P.C., Brzozowski, T. and Konturek, S.J. 2011. Stress and the gut: pathophysiology, clinical consequences, diagnostic approach and treatment options. Journal of Physiology and Pharmacology. 62(6):591-599.

  11. Farzi, A., Frohlich, E.E. and Holzer, P. 2018. Gut microbiota and the neuroendocrine system. Neurotherapeutics. 15(1):5-22.

  12. Martin, C.R., Osadchiy, V., Kalani, A. and Mayer, E.A.. 2018. The Brain-Gut Microbiome Axis. Cellular and Molecular Gastroenterology and Hepatology. 6(2): 133-148.

  13. Bray, N. The microbiota-gut-brain axis. Nature Research. Accessed from:

#health #wellness #naturopathicdoctor #naturopath #meditation #microbiome #naturopathy #gutmicrobiome #naturopathicmedicine #gut

bottom of page