How meditation affects your gut

As part of our Biohacking Masterclass Series, we will explore a number of different techniques and practices to improve your daily performance. This series will range from obvious subjects like exercise and nutrition to fringe subjects like breathing techniques and sleep hygiene. Consult your physician before implementing any of these topics. We are not your physician. Note: This post may contain affiliate links to the products we use. 

In the past we have discussed the role of the autonomic nervous system (ANS) in the human stress and relaxation response. The ANS is a sensitive scale balanced between the parasympathetic and sympathetic subsystems. We will provide a more detailed description of each arm of the ANS below, but the interplay between these two branches has far-reaching effects in the body. In fact, a common imbalance with an overpowering sympathetic nervous system can go as far as changing the ratios of bacteria in your gut or alter your body’s immune response. How can you use specific tools to counterbalance an overactive state? Can these tools go as far as optimizing and diversifying your gut microbiome? 

In order for you to have a proper understanding of the two ends of the spectrum within the overarching autonomic nervous system, we will provide a brief overview below. If you have a good understanding of this scale, skip this section. 

The Parasympathetic and Sympathetic Nervous System

The parasympathetic nervous system is responsible for rest and relaxation. When active, this state is characterized by a low heart rate, proper digestion, and a release of serotonin and oxytocin (happiness hormones). 

On the other hand, activation of the sympathetic nervous system promotes alertness and readiness for action. Sympathetic states are responsible for the ‘fight or flight’ stress response that is characterized by an adrenaline rush, heightened heart rate, decreased digestion, clammy hands, and more. 

Normally, the body will maintain a general state of parasympathetic activation until the sympathetic nervous system is required. In modern times, we have fewer instances where we are required to fight or run for our lives, and those sympathetic cues are more commonly found in the office, on the playing field, or during sales calls. 

Once the sympathetic nervous system is activated, it should be used to help you execute the task at hand. Upon completion of said task, the sympathetic nervous system should ‘back off’ and the parasympathetic nervous system should counterbalance and provide a sense of relaxation and rest. 

The issue is, these stressors are frequently experienced unconsciously, where we are not entirely aware of our increasingly activated sympathetic response. When we string together several days of this ‘stressed out’ state, we begin to take away from our body’s relaxation and restoration phases. 

The Role of Stress in the Gastrointestinal Tract

Recent findings have connected this sustained stress response to significant changes in the gastrointestinal tract, including the transition into disease states. The neurotransmitters responsible for the stress response, what we will call “stress molecules”, have direct actions on the cells within the gastrointestinal system. 

Release and binding of these stress molecules lead to some of the following effects in the gut [1-3]: 

  • Impaired mucosal barrier to enteric bacteria
  • Increased adherence of pathogens within the gut
  • Increased uptake of potentially pathogenic bacteria 
  • Increased intestinal permeability 

Rebalance Your ANS Using Meditation

As discussed above, the sympathetic nervous system is counterbalanced by the parasympathetic nervous system. This back-and-forth “dance” between these two systems helps maintain optimal performance throughout the body, not just in the GI system. 

There are many techniques that fall under the overarching umbrella of “parasympathetic activators”, but one of the most powerful tools researchers discuss is meditation. Meditation is capable of swinging the nervous system back into balance and of reducing the release of the previously mentioned “stress molecules”. 

Strategic use of meditation can reduce chronic inflammation and help maintain healthy gut barrier function. [4]

If you are new to meditation, read our quick breakdown about two different types of meditation and their effects on thinking states here. If you want fine-tuned, accurate recall, you will want to use a different practice than another individual who is after more creative, open thinking states. 

If you want to further optimize your gut microbiome, see our article on the role of exercise and bacterial diversity in the gastrointestinal tract here

If you want to eliminate another source of GI stress, avoid these common food additives/emulsifiers


  1. Lyte M, Vulchanova L, Brown DR. Stress at the intestinal surface: catecholamines and mucosa-bacteria interactions. Cell Tissue Res. 2011 Jan;343(1):23-32. doi: 10.1007/s00441-010-1050-0. Epub 2010 Oct 13. PMID: 20941511. 
  2. Bailey MT, Dowd SE, Parry NM, Galley JD, Schauer DB, Lyte M. Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium. Infect Immun. 2010;78(4):1509-1519. doi:10.1128/IAI.00862-09
  3. Cogan TA, Thomas AO, Rees LE, Taylor AH, Jepson MA, Williams PH, Ketley J, Humphrey TJ. Norepinephrine increases the pathogenic potential of Campylobacter jejuni. Gut. 2007 Aug;56(8):1060-5. doi: 10.1136/gut.2006.114926. Epub 2006 Dec 21. PMID: 17185353; PMCID: PMC1955515.
  4. Househam AM, Peterson CT, Mills PJ, Chopra D. The Effects of Stress and Meditation on the Immune System, Human Microbiota, and Epigenetics. Adv Mind Body Med. 2017 Fall;31(4):10-25. PMID: 29306937.