Dr. Ariel Jones, ND

The Gut/Brain Connection

Irritable bowel disease (IBD) includes Ulcerative Colitis (UC) and Crohn’s Disease (CD). It is one of the 5 most prevalent gastrointestinal diseases in the United States.1 People with IBD and other gastrointestinal diseases like Irritable Bowel Syndrome (IBS) suffer from the effects of damaged gut tissue due to inflammation. The symptoms are often life altering, painful and chronic.

The gut and the brain are highly integrated. They communicate bi-directionally through the Autonomic Nervous System (ANS) and the Endocrine HPA (hypothalamus/pituitary/adrenal) axis using serotonin, tryptophan, cortisol, epinephrine and norepinephrine.2 Feedback from the gut goes to the emotional motor system (EMS) in the brain, also known as the limbic system. Since there is bi-directional communication, it is important to understand the role of the limbic system to understand how the two interact. The limbic system is responsible for both the internal and external homeostasis of the organism. When there is an internal or external event causing imbalance, the limbic system senses this and releases hormones into the body to rebalance. The limbic system facilitates survival, threat avoidance, social interaction and learning. Emotions are generated here and the associated physiological changes are the work of the limbic system. The limbic system is involved in the ‘top–down’ modulation of visceral pain transmission as well as visceral perception1. The limbic system is the traffic control center where the brain and gut interface and interact.

What happens in gut disease?

The causes of IBD have 4 hypothesis: genetic predisposition, environmental triggers, immune system hyperactivity, and chronic inflammation. The concordance rate in identical twins is 10-15% for UC and 30-35% in CD, demonstrating that non-genetic factors may have a large role in disease development.3

Different environmental factors have been identified:2

  1. Psychosocial stressors activate stress circuits within the EMS leading to physiological gut responses via the Autonomic and Endocrine systems. EMS output causes corticotropin-releasing factor (CRF), cortisol, norepinepherine and epinephrine to be released. These molecules shifts the immune system towards a Th2 response: increased mast cells, nitric oxide synthase expression.
  2. Autonomic responses can directly or indirectly modulate the gut’s permeability to antigens (foreign particle) and microbes (bacteria). When the gut’s permeability increases in response to antigens and bacteria, the immune system activates to protect our bodies from the foreign invaders. A highly permeable gut can lead to gut hyperpermeability disorder a.k.a. Leaky Gut.
  3. Physical Stressorssuch as antigen and bacteria modulate gut immune function, and immune products from the gut such as cytokines and chemokines create inflammation and pain seen in IBD.

UC is characterized by inflammation limited to the colon region of the intestine. CD can involve any part of the digestive tract but is most commonly found in the terminal ileum or perianal region. CD is associated with complications such as strictures, abscesses and fistulas.4

The Intestinal Mucosa is important

The intestinal mucosa is very important to gut health. Its functions are nutrient absorption, physical barrier and signal-transduction. It senses its environment and secretes regulatory products in response. The digestive tract also contains the largest component of the immune system in the human body2. People with IBD have a disrupted intestinal mucosa. Without a healthy mucosa bacteria seep into the blood stream initiating an immune response that leads to chronic, damaging inflammation and pain.

An astounding fact is that 95% of our serotonin is made in the gut. Serotonin is responsible for our subjective feeling of happiness and good mood. If our gut tissue is not healthy, we can not make adequate serotonin.5

Painful inflamed gut alters the brain: Depression and IBD

As mentioned earlier, gut control is chiefly within the limbic system in the brain. It is also where emotions, physical and sexual drive, sleep, appetite, memory processing, stress response and mood disorders are controlled. When there is a homeostatic imbalance like pain or inflammation due to IBD, the limbic system responds to rebalance the system. The activities in the limbic system are so important and ubiquitous to the functioning of a human being that disturbances in any part can alter and affect mood and behavior.

One of the changes seen in the brain of patients with acute colitis is the upregulation of Neuropeptide Y (NPY).6 For the most part, NPY seems to be a protective and helpful response to pain. One study shows that NPY is part of the mechanism that helps mammals recover from intense pain associated with inflammation or nerve injury.7 NPY is also responsible for reducing anxiety and stress, modulating sleep/wake cycles, reducing voluntary alcohol intake, lowering blood pressure, and controlling epileptic seizures.8,9 The role of NPY in increasing food intake and storage of energy as fat can become detrimental if it is chronically stimulated. In addition to pain and inflammation, stress, high fat and high sugar diet has also been shown to increase NPY levels in the brain.10 NPY upregulation is a function of IBD and one of the links between IBD and depression.

Today, there is strong evidence to support the connection between IBD and depression. Depression has been shown to occur 1 year, or less, before a diagnosis with UC, meaning that symptoms of undiagnosed UC cause depression, or conversely, that the occurrence of depression may be a cause of UC.11 In any case, they are concurrent. Anxiety and depression are more common in patients with IBD and their symptoms are more severe during periods when the disease is active. Additionally, the course of the disease is worse in depressed patients. Treatment with corticosteroids, a common treatment of choice for patients with IBD, can induce mood disorders or other psychiatric symptoms.12

The link between the gut and mental health is clear. There has never been more reason to treat and heal the gut for patients with gut inflammation or mental disorders. So lets get started.

Healing the gut to improve depression

  1. Remove Stressors

Physical stress like a nutrient poor diet, processed foods, history of antibiotic use or too much sugar damages the gut and weakens our immune system. Not getting enough sleep is a physical stress. Emotional stress can include our job, money, primary relationships and more. Identifying what causes you stress is a good first step on the road to wellness. Working on how to decrease stressors is an ongoing process. Utilize family and close friends to identify and mitigate stressors in your life.

  1. Clean Up The diet

Most importantly and easily is the removal of pro-inflammatory foods that we don’t need and are expensive and detrimental to health. There are many foods that cause inflammation by being allergenic or toxic or both.

Removing Processed foods: anything that comes in a box or can is processed. Processed foods are lower in nutrition than fresh, whole foods, and are made with a variety of ingredients that do not support good health, like GMO’s, high fructose corn syrup, preservatives to name a few. There are many whole foods options in the grocery store that are just as easy to consume, and cheaper that buying processed, pre-made food. Consider eliminating packaged frozen meals, packaged cookies, granola bars, frozen pizzas, french fries, hot dogs, deli meats, potato chips, candy bars, soda, salad dressings, ice cream, instant noodles and Kraft dinner. Whole foods are the fruits, vegetables, nuts, grains and seeds we see in their natural forms. They are often located on the perimeter of a grocery store. Substituting whole foods for processed foods will make a big difference in your health. Just ask Dr. Terry Wahls, MD. She healed herself from MS using whole foods, and you can see her TED Talk here: https://www.youtube.com/watch?v=KLjgBLwH3Wc

Eliminating Pesticides: remove pesticides from your diet by buying exclusively organic or washing your fruits and vegetables in a water/vinegar mixture of (10:1). Some of the more fatty foods like nuts need to be bought organic because they absorb pesticides more readily than fruit or veggies with a water resistant peel.

Add in foods that are gut healing: flax seeds and chia have a mucilaginous, gooey coating that is healing for gut tissue, contain fiber, protein and omega 3 fatty acids which help to bulk up stool for elimination and decrease inflammation respectively. Flax seeds can be made in to delicious crackers, taken as oil, or ground up and put into oatmeal. When soaked, chia becomes chewy and can make an excellent pudding. Cabbage contains the amino acid glutamine which helps to heal the enterocytes, or cells of the GI tract. Raw cabbage can be grated into salads or eaten as a slaw.

Nut soaking helps to neutralize the phytic acid found in the outer later of nuts. Soaking nuts and seeds for 6 hours before eating makes it easier on the intestines to digest and absorb their nutrients.

Rinsing your grains before you eat them helps to remove the saponins found on their outer surface. Saponins bind to the mucosal epithelium and increase surface permeability. Too many saponins and other gut toxins can lead to leaky gut.

  1. Heal The Gut: Supplementation

– Glutamine: food for enterocytes.

Lactobacillus helveticus and Bifidobacteria longum: have been shown to help IBD, while B. infantis relieves many of the symptoms of IBS.15

– Fish oil: to decrease inflammation and support cognitive functioning of the brain.

Herbs:Ulmus fulva (slippery elm),Glycyrrhizaglabra (licorice), Althea officinalis (Marshmallow), Avena sativa (Oats).

  1. Support Adrenal Glands

Since cortisol is expended during the homeostatic process, long-term stress can lead to cortisol resistance and adrenal fatigue. You can support the adrenal glands using vitamins like B5 and C, herbs and homeopathy.

  1. Social Support

Reaching out to people in your community, family and friends is an important part of maintaining good mental health. Social support lowers, stress, anxiety and depression and improves outcome for patients with IBD.16

Raw Food Recipes to Heal The Gut

Chia Pudding


  • 1 can coconut milk
  • ½ cup chia seeds
  • 1 tsp vanilla
  • 1 tbs maple syrup
  • 1 dash cinnamon


Add ingredients into coconut milk, stir well with a fork or wisk. Leave covered in the fridge. Stir again in 20 minutes to break up chia seeds. Serve in a dish cold with fresh or frozen fruit.

Flax crackers


  • 1 cup golden flax
  • 1 cup brown flax
  • 2 tbs chia
  • 1 tsp honey

Add ins (optional):

  • 1/4 cup sesame seeds/pumpkin seeds
  • 1/4 cup nuts (almond, walnut, pecan, macadamia)
  • 1/4 cup dried berries (currants, raisins, cranberries, blueberries)
  • Herbs: Rosemary


Soak the flax and chia and seeds for 20 mins until the mixture is gelatinous. Add in any spices, nuts or berries. Lay flat 1 cm on a dehydrator with nonstick sheet for 10-12 hours. Perfect as a snack by themselves or with spreads like hummus.

Flax Salad Dressing

  • 1 part flax oil
  • 1 part lemon juice
  • chopped garlic
  • Any herbs you like: chives, dill, parsley
  • Pinch of sea salt


Add into a glass container and store in fridge.

Jones_headshotDr. Ariel Jones is a native of Vancouver BC and a graduate of BINM (2013). Her practice emphasizes removing the physical, mental and spiritual obstacles to cure while implementing a toxin-free lifestyle for raw, radiant health. Ariel has enjoyed living in Victoria, BC during her BSc. in biology and psychology, Calgary AB and Hilo Hawaii for a post-graduate residency focused on raw food diet, detoxification, addictions and cancer therapies.



  1. Weiner, G. Where The Rubber Meets the Road: Treating Inflammatory Bowel Diseases – NaturalPath. NaturalPath. 2014. Available at: https://naturalpath.net/body/gastrointestinal-health/where-the-rubber-meets-the-road-treating-inflammatory-bowel-diseases/. Accessed March 17, 2015.
  2. Jones , MP, Dilley, JB, Drossman, D, Crowell, MD. Brain–gut connections in functional GI disorders: anatomic and physiologic relationships. Wiley Online Library. 2005. Available at: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2982.2005.00730.x/full. Accessed March 17, 2015.
  3. Khor, B, Gardet, A, Xavier, RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature. 2011. Available at: http://www.ncbi.nlm.nih.gov/pmc/articles/pmc3204665/. Accessed March 17, 2015.
  4. IBD etiology and pathophysiology. 2013. Available at: https://www.ibdinsights.com/about/etiology-pathophysiology/. Accessed March 17, 2015.
  5. Cowen, PJ. Cortisol, serotonin and depression: all stressed out?. BJPsych. 201. Available at: http://bjp.rcpsych.org/content/180/2/99.short. Accessed March 17, 2015.
  6. Pucar Batici, L, Detel, D, Kucic, N, Buljevic, S, Verljen, J. CD26 deficiency alters VIP and NPY levels in murine Crohn-like colitis. Congress of the Croatian Society of Biochemistry and Molecular Biology. 2014. Available at: http://bib.irb.hr/prikazi-rad?lang=en&rad=727332. Accessed March 17, 2015.
  7. Solway, B, Bose, SC, Corder, G, Donahue, RR, Taylor, BK. Tonic inhibition of chronic pain by neuropeptide Y. NCBI. 2011. Available at: http://www.ncbi.nlm.nih.gov/m/pubmed/21482764/. Accessed March 17, 2015.
  8. Tatemoto K (2004). “Neuropeptide Y: History and Overview”. In Michel MC. Handbook of Experimental Pharmacology 162. Springer. pp. 2–15
  9. Colmers WF, El Bahn B (2003). “Neuropeptide Y and Epilepsy”. Epilepsy Currents/American Epilepsy Society 2 (3): 53–8. doi:10.1046/j.1535-7597.2003.03208.x. PMC 321170. PMID 15309085.
  10. Maugh ll, TH. Research points to way to eliminate belly fat. Chicago Tribune. 2007. Available at: http://articles.chicagotribune.com/2007-07-02/news/0707010371_1_dr-zofia-zukowska-mice-and-monkeys-show-npy. Accessed March 17, 2015.
  11. Kurina, LM, Goldacre, MJ, Yeates, D, Gill, LE. Depression and anxiety in people with inflammatory bowel disease. Journal of Epidemiology Community Health. 2001. Available at: http://jech.bmj.com/content/55/10/716.full. Accessed March 17, 2015.
  12. Graff, LA, Walker, JR, Bernstein, CN. Result Filters. National Center for Biotechnology Information. 2009. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19161177. Accessed March 17, 2015.
  13. Amilleri, M. Serotonin in the Gastrointestinal Tract. Current opinion in endocrinology, diabetes, and obesity. 2010. Available at: http://www.ncbi.nlm.nih.gov/pmc/articles/pmc2694720/. Accessed March 17, 2015.
  14. Lakhan, SE, Kirchgessner, A. Neuroinflammation in inflammatory bowel disease. JNI. 2010. Available at: http://www.jneuroinflammation.com/content/7/1/37. Accessed March 17, 2015.
  15. Whorwell, PJ, Altringer, L, Morel, J, et al. Efficacy of an Encapsulated Probiotic Bifidobacterium infantis 35624 in Women with Irritable Bowel Syndrome. Naturecom. 2006. Available at: http://www.nature.com/ajg/journal/v101/n7/abs/ajg2006294a.html. Accessed March 17, 2015.
  16. Sewitch, MJ, Abrahamowicz, M, Bitton, A, et al. Psychological distress, social support, and disease activity in patients with inflammatory bowel disease. Naturecom. 2001. Available at: http://www.nature.com/ajg/journal/v96/n5/abs/ajg2001352a.html. Accessed March 17, 2015.
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