The gut-brain axis, the microbiome, and chronic disease development


What I’d like to focus on with this article is a major network of disease causation and progression involving the gut-brain axis, the gastrointestinal microbiome, and inflammatory cascades.

The enteric (meaning of the gut) nervous system’s connection to the central nervous system is often referred to as the “gut-brain axis.”  The interplay between the enteric nervous system (ENS) and the central nervous system (CNS) helps regulate many processes, but a few of them include: gut motility, blood flow, fluid exchange, bile and stomach acid secretion, and digestive enzyme production [1].  As a bit of a side note, the ENS possesses strong communication links with the limbic system (which is why psychological and emotional stress can easily impair gut health and function) as well as with many skeletal muscles, particularly those around the abdomen (which is why a proper postural carriage, proper movement programming, and healthy exercise habits are very important for normal gut function).

Essentially, the ENS and CNS work together to help meet the physiological demands of the body.  The ENS also provides a significant medium through which the GI microbiota (the collection of microbes inhabiting the gut) communicates with the CNS.  The most important point regarding this communication pertinent to this article’s objective is the fact that the microbiota plays a huge role in determining the immune system’s activity level and the extent of inflammatory mediation throughout the body [2].  How many chronic disease conditions bloom from persistent inflammation?  A lot, in fact most of them.

The health of and diversity among the species comprising the human microbiome are of great importance to one’s well-being.  Everyone’s microbiome is unique to them, and everyone’s genetic blueprint helps to establish the unique microbial “soil” through which their garden of health grows.  Given the very large amount of environmental and dietary pollutants we are subjected to on a daily basis, the average microbiome is usually in notable disarray.  While a myriad of commensal, symbiotic, and even pathogenic relationships exist among the microorganisms we harbor, a fairly delicate balance among them needs to be maintained in order for health to be expressed.

Dysfunctional populations of microbes (bacteria, fungi, parasites, protozoa) comprising the GI microbiome and intestinal inflammation can break down the lining of the intestinal wall, leading to “Leaky-gut syndrome” or intestinal hyperpermeability.  Once the intestinal wall becomes excessively permeable, microbes, toxins, and undigested food particles leaking out of the gut can overstimulate the immune system and exhaust the adrenal glands and the liver as these organs have to respond to the flood of antigens entering the bloodstream, lymphatic circulation, and extracellular matrices [3].  Once Leaky-gut has developed, pro-inflammatory cytokines from the gut can be transported to the brain after breaching the blood-brain barrier and invoke inflammation of the glial cells within the brain, thus increasing the body’s “inflammatory set-point” [4] [5].  A raising of the body’s inflammatory set-point easily paves the way for the development of chronic degenerative disease and/or autoimmune conditions.  At this point, immune-mediated inflammatory responses become especially disruptive to cellular membranes, which not only disrupts cellular function directly, but also contributes to hormonal imbalances as the hormone receptors embedded within cellular membranes become muddled or damaged due to the inflammation.

So what can lead to dysbiosis and intestinal inflammation?  Many things but a few that are at the top of the list include the following:

  • Pharmaceutical antibiotic use or ingestion of antibiotics from conventionally-raised livestock.
  • GMO food consumption due primarily to the glyphosate contained within (you can thank Monsanto for this) [6].
  • A large amount of hybridized grain consumption, particularly wheat.
  • Consumption of high fructose corn syrup, artificial sweeteners, and sugar alcohols such as xylitol and erythritol [7] [8].
  • Pesticide, fungicide, herbicide, and rodenticide consumption from non-organic produce.
  • Not consuming enough prebiotics to feed the good bacteria.
  • Excessive intake of conventional, processed (pasteurized and homogenized) dairy products. This is largely due to the beta-casomorphin-7 metabolite of the beta-casein protein found in A1 cow’s milk being able to elicit a nearly identical immune response as that invoked by the ingestion of gluten [9].
  • Drinking water that has not been filtered of chlorine as such chlorine can kill off beneficial bacteria in the gut [10].
  • Repressing or avoiding emotions.
  • Tension and inflammation in the myofascial system as such inflammation can be transferred to the GI tract and other organs via what are termed “somato-visceral” reflexes.

Now, correcting the condition of dysbiosis and intestinal inflammation can be a bit complex depending upon the person and their unique etiology.  For instance, if the individual has a fungal overgrowth, a bacterial or parasitic infection, significant nutrient deficiencies, significant toxin accumulation, or they are harboring unresolved grief or anger, the resolution plan will be different.  However, generally speaking, and if nothing else needs to be addressed first, the plan would revolve around removing populations of pathogenic microbes (with nutritional and herbal approaches), healing the lining of the intestinal wall, and then recolonizing the gut with prebiotic and probiotic interventions.  Once the gut microbiome is restored to normal, the body can begin healing itself of inflammatory over-activity as the pressure is taken off of the adrenals, the liver, the central nervous system, and the immune system.

I hope this was helpful for you!

Author bio:

Denton Coleman is an Exercise Physiologist and is the founder of Satori Institute, an online holistic health, wellness, and fitness academy.  You may visit the Institute at or if you’d simply like more information on the concepts discussed in this article you may take a look at the Institute’s treatise on holistic nutrition, available here.


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  2. Neufeld, K. M., Bienenstock, J., & Foster, J. A. (2008). The impact of intestinal microbiota on anxiety-like behaviour. Neurogastroenterol Motil20, 125.
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  4. Tracey, K. J. (2002). The inflammatory reflex. Nature, 420: 853–859.
  5. Tips, J. (2015). The Bidirectional Gut-Brain/ Brain-Gut Axis New Findings: Neuro/Microbiota Colloquy and Holistic Healing. The American Chiropractor, (November), 44-51.
  6. Mesnage, R., Defarge, N., Spiroux de Vendômois, J., & Séralini, G. E. (2014). Major pesticides are more toxic to human cells than their declared active principles. BioMed research international2014.
  7. Malik, V. S., Popkin, B. M., Bray, G. A., Després, J. P., Willett, W. C., & Hu, F. B. (2010). Sugar-sweetened beverages and risk of metabolic syndrome and type 2 diabetes A meta-analysis. Diabetes care33 (11), 2477-2483.
  8. Blaut, M., & Clavel, T. (2007). Metabolic diversity of the intestinal microbiota: implications for health and disease. The Journal of nutrition, 137 (3), 751S-755S.
  9. Elliott, R. B., Harris, D. P., Hill, J. P., Bibby, N. J., & Wasmuth, H. E. (1999). Type I (insulin-dependent) diabetes mellitus and cow milk: casein variant consumption. Diabetologia42 (3), 292-296.
  10. Homonnay, Z. G., Török, G., Makk, J., Brumbauer, A., Major, É., Márialigeti, K., & Tóth, E. (2014). Bacterial communities in the collection and chlorinated distribution sections of a drinking water system in Budapest, Hungary. Journal of basic microbiology54 (7), 729-738.
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Denton Coleman
Exercise Physiologist
Denton Coleman is an Exercise Physiologist and Medical Researcher. He is the founder of Vanguard Health and Fitness, which disseminates leading-edge, upper echelon information and curricula regarding nutrition, fitness, and holistic wellness. You may visit Vanguard Health and Fitness at