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The Digestive System: Revealing Hidden Facts of Your Overall Health.

Annalies Corse BMedSc, BHSc, ND

Written for and originally published by the MINDD Foundation:

For most people, the digestive system serves as the repository for delivering food to the body, and eliminating waste. We may never give thought to the impressive amount of physiological effort and biochemical work necessary for this to take effect. Most people are not troubled by major digestive pathologies. We enjoy our food, and we get on with life.

Do other small ailments plague your everyday experiences of good health and wellbeing? Are these complaints you simply put up with, or are they major health conditions? Would you feel better if you had more energy? Is your immune system not as resilient as it should be? Are you prone to atopic conditions, such as allergies and eczema? Do you have signs of endocrine dysfunction, fertility issues, or autoimmune disease? Is your mental and emotional health in need of support? All of these are linked to poor digestive health. This list reads like a marketing campaign for the latest ‘cure all’ supplement. However, there is good reason for this; basic scientific principles explain exactly why digestive health is critical to the health of an entire organism. Ask any Naturopath, Integrative Doctor or holistic Nutritionist what is the most important system in the human body and you are most likely to hear the same response: The Digestive System. It is why the MINDD Foundation is so notably focused on how to attain and maintain enduring Digestive health, at any age.

Anatomy and Physiology

The human digestive tract is purpose built for every aspect of digestion. The anatomy of the digestive tract actually changes as it descends from the oral cavity, all the way down to the rectum and anus:

  • Oral cavity: a cavity lined with a thick and stratified epithelium, perfectly suited to with standing mechanical and harsh pressures from chewing and swallowing. The oral mucosa is supported heavily by salivary glands and blood vessels. Saliva is a complex fluid of water, electrolytes, mucous, antibodies, and digestive enzymes. Signs of poor digestive health in the oral cavity include halitosis (bad breath), some dental problems, ulcerations, oral infections and abnormal coatings on the tongue
  • Oesophagus: again lined by a stratified epithelium that secretes mucous and has a high cell turn over of desquamation. This desquamation or cell ‘sloughing’ is necessary in the mouth and oesophagus to replace tissue damaged by temperature extremes, mechanical and chemical trauma. Smooth muscle layers facilitate swallowing and peristalsis. Signs and symptoms of poor digestive health in the oesophagus include acid reflux, gastro-oesophageal reflux disease, difficult or painful swallowing and inflammation (oesophagitis).
  • Stomach: a highly specialised and thick muscular organ. Mucous must be secreted here to protect the stomach from the low pH of gastric secretions (the low acidic pH here is fundamental to healthy and thorough digestion). Muscle layers are thicker in the stomach, to facilitate strong contractions for the mixing and churning required for both mechanical and chemical digestion. Signs and symptoms of poor digestion originating in the stomach include acid reflux and excessive belching. Achlorhydria (low stomach acid) is rather prevalent in the population. Gastric ulcers and gastritis are another well-known diseases, often induced by diet, stress and infection.
  • Small Intestine: the site of nutrient absorption. Specialised anatomical modification of the mucosa (known as villi, microvilli and lacteals) facilitate the absorption of monosaccharides (simple sugars), amino acids (from proteins) and fatty acids (from lipids). Significant amounts of enzyme secretion to facilitate chemical digestion. Facilitated by smooth muscle contractions for peristalsis. Vast surface area of villi and microvilli network to enhance absorption. Heavily influenced by the health of the nervous system, via the enteric plexus. Influences the health and functionality of the immune system, via gut associated lymphoid tissue located predominantly in the ileum, but also found in other areas of the digestive tract. Signs of poor digestive health and disease here include allergies, atopy, Coeliac disease, malabsorption, obesity and IBS, through to major immune, developmental and mental health conditions.
  • Appendix: the forgotten and neglected appendage of the digestive tract. New research is revealing that the appendix might be a reservoir for beneficial species of good/healthy gut bacteria. It may also be involved in immune responses, hence the volatile reactions noted with appendicitis.
  • Large Intestine: essential functions include the absorption of water and many vitamins. Digested, unabsorbed food is converted to faecal material. Thick walls of smooth muscle facilitate powerful contractions for the defecation reflex. Gut bacteria perform fermentation reactions on complex sugars indigestible to humans, helping to release nutrients from these foods such as vitamins, B1, B2, B6, B12 and vitamin K. Constipation, bloating, flatulence and diarrhoea are all multifactorial in nature, but indicate problems with the large intestine. Other diseases of poor large intestinal health include ulcerative colitis, and any significant signs such as blood and mucous in the stool.

The microbiome

 No discussion of human digestive health is complete without mention of the microbiome. The human microbiome consists of all the genes of the microorganisms living in and on the human body. The vast majority of these microbes reside in our digestive system. Think of the human microbiome as the microbial counterpart of the human genome. Without question, the advances in this area of medical science are incredibly important to health; we will likely see many future chronic disease treatment protocols based around gut health and the microbiome. Obesity, allergies, cancer, autoimmune disease, depression and even Alzheimer’s’ disease all show links to unhealthy gut microbes and a poor quality microbiome. The microbiome population changes rapidly in response to the type of diet we eat, thus nutritional medicine and nutritional counselling is paramount to gut health. For a recent MINDD article on the specifics of the human microbiome, including what to eat, please see

All disease begins in the gut

“All disease begins in the Gut” – Hippocrates

The iconic figure of both ancient and modern medicine coined this phrase over 2000 years ago, yet it seems nothing could be truer today. In a recent book (Gut: The Inside Story of Our body’s Most Under-rated organ), doctor and scientist Giulia Enders explains that we need to stop treating people as having skin conditions, mental health conditions, immune conditions, etc., and start recognising skin, emotional, immune and a host of other pathologies as patients with intestinal problems. This has indeed been the approach of Naturopathic medicine for thousands of years; fortunately, modern medicine is beginning to accept this approach and provide valuable evidence to support naturopathic and integrative health protocols.

Top 5 take away clinical pearls for gut health

  1. Try not to consume large amounts of liquids with meals. Sips of water are OK to as you get used to this change. Copious amounts of water with food dilute the digestive secretions that contain the acids, hormones and enzymes required to digest food thoroughly and correctly. Adequate water is often secreted by the digestive tract as you digest food, so the need to add more is unnecessary.
  2. As much as you can, chew your food slowly and thoroughly. Take time to eat your meals, at least 20 minutes. Far too many people ‘inhale’ a large meal in less than 5 minutes. Preparing, smelling, touching and tasting food as you cook is incredibly strong sensory stimulation for your brain; the process of digestion has literally begun before you take your first bite. A note to parents of young children: it is hard to eat slowly when you have no time. At least attempt to do this one meal per day. Sit down and enjoy 30 minutes of actual slow eating with your family, at as many meals as you can.
  3. Try not to eat when under stress, or address any chronic stress issues. Under the effects of stress hormones and nerve impulse transmission, blood is diverted away from digestive organs during the stress response. Digestion is deemed unnecessary when other organs such as skeletal muscle and the heart need high blood circulation during the stress response. This lack of blood circulation to digestive organs is incredibly counterproductive to good digestion, diminishes peristaltic activity of smooth muscle decreases secretions involved in chemical digestion, absorption and transport of nutrients across the gut wall in to the blood stream and lymphatics.
  4. Make healthy defecation a priority. This may seem crude or embarrassing to consider, but it is essential to your health on every level. Good quality, healthy stools (faeces) are simple to achieve with the right diet and lifestyle choices. We should all pass 1-3 formed stools each day. If you are regularly constipated, have frequent diarrhoea, loose motions, blood or mucous in the stool, it is vital you seek help from a Naturopath, Nutritionist or Doctor to receive assistance on normalising your bowels through diet and lifestyle practices. Familiarise yourself with the Bristol Stool chart, an insightful and incredibly simple piece of health and medical education.
  5. Consider your diet and where it needs to be overhauled. Diets for healthy digestion are not a one-size approach; the diets we all need for gut health are often unique and tailored to suit our individual needs. Certain food groups may require elimination. To avoid nutrient deficiencies, this should be done with the guidance of a health professional. In general, we need to keep very hydrated between meals with water, fruits, vegetables and herbal tissanes. We need to eat complex carbohydrates and fibre. We need to look at our medications; some digestive problems are a known side effect of specific pharmaceuticals. Reaching out to an integrative health practitioner for a prescription of probiotic strains for your specific health needs is wise. This is especially true if you were born via caesarean section, could not be breastfed, or have had a long history of antibiotic use.


  1. National Institute of Allergy and Infectious Diseases (NIAID). The Human Microbiome. The Genetic Science Learning Centre, University of Utah. Available at:
  2. Anders, R. (2011). Functional Histology of the Gastrointestinal Tract. Lecture. Johns Hopkins Pathology. Available at:
  3. Janeway, CA Jr.; et al. (2001). “The mucosal immune system”. Immunobiology. New York: Garland Science. 10-13.
  4. Kuo, B. (2006). Oesophagus- anatomy and development. GI Motility online. Available at:
  5. Tiwari, M. (2011). Science Behind Human Saliva. Journal of Natural Science, Biology and Medicine. Jan-Jun; 2(1): 53-58.
  6. Zahid, Aliya (2004-04-01). “The vermiform appendix: not a useless organ”Journal of the College of Physicians and Surgeons–Pakistan: JCPSP 14 (4): 256–258.