Is Poor Digestion Affecting Your Mood?

Dysbiosis, Digestion, the Gut-Brain Axis and Your Mood
Graphic of a women putting a hands on her head

Medically Reviewed by Dr. Emma Pollon-MacLeod, ND

It is known that mood and stress can have a significant impact on digestion. Many of us may have had one experience wherein our tummy is turned upside down due to some form of stress. That said, what if there was a direct correlation between your mood, the state of your digestion and your stress response?

Would you be surprised if I told you there was? Well, there is and it is pretty complex. So, take a deep breath and put on your “scuba gear” because we’re going to dive deep into the gut-brain axis and discover its implications on mood, digestion, stress, cognition, immunity and inflammation.


What is the Gut-Brain Axis?

The gut-brain (GB) axis is a highly complex communication matrix that involves multiple biochemical systems. Simply put, it is a two-way biochemical signalling between the microbiome and the brain and is mediated by the enteric nervous system through the vagus nerve. Think of it like an old-school copper wire phone network. The brain is a phone and lives in the north. The gut and its microbiome are also a phone and live in the south, but they constantly call each other and send biochemical messages through “vagal” phone wires. Interestingly, the microbiome is responsible for the majority of conversation between the phones and the type of conversation is dictated by whether there is balance, i.e., symbiosis within the gut flora or dysbiosis.

To expand further, data has confirmed that Bifidobacterium and Lactobacillus have a positive effect on mood which is why they are known as “psychobiotics.” In a six-week clinical trial with petrochemical workers, groups receiving a probiotic capsule (containing L. casei, L. acidophilus, L. rhamnosus, L. bulgaricus, B. breve, B. longum, and Streptococcus thermophiles) or probiotic yogurt (containing B. lactis and L. acidophilus) showed alleviated anxiety and depression compared to groups receiving a placebo capsule or conventional yogurt.1 Further, butyrate appears to have neuroprotective properties and has been demonstrated to have antidepressant potential in animal models.2

Moreover, because the vagus nerve acts like a switch between your body’s sympathetic (fight or flight) and parasympathetic (rest and digest) systems,3 it is directly involved in the hypothalamic-pituitary-adrenal (HPA) axis which governs your stress response and ties it into the GB axis. The immune system is also a major component of the GB axis, due to the role microbiota play in regulating and activating immune cells.


The Microbiome, Cortisol and the Stress Response

Cortisol is a steroid hormone produced by the adrenals. It is the main hormone involved in the HPA axis which is why it is often referred to as the “stress, or fight or flight” hormone. Cortisol is involved in a series of regulatory processes in the body. That said, when your levels become too high or too low, problems can arise, particularly when levels are elevated due to chronic stress. Activation of the HPA axis by stress leads to cortisol secretion. It can affect gut integrity, motility and mucous secretion, leading to changes in the composition of the gut microbiota.1 These changes lead to a damaged microbiome, i.e., dysbiosis which drives the weight gain, anxiety and depression that often accompany high stress.

Except for diet, lifestyle and environmental factors, there is also evidence that the “programming” of the HPA axis appears to begin in childhood; therefore, early life trauma very much defines the architecture of the stress response and microbiome in adulthood. Interestingly, gut dysbiosis in IBS correlates not just with GI symptoms, but also with regional brain volumes and early life trauma.4

Even more interesting is the direct link to specific bacteria strains and how sensitive one is to stress. In short, an abundance of unhealthy gut bacteria will signal a significant release of cortisol with a heightened stress response. Conversely, an abundance of healthy bacteria creates less cortisol secretion and a resilient response to stress. Lastly, seeing we inherit our microbiome at birth, its condition will impact how one responds to stress at a young age—furthering informing the development of the HPA axis and stress response. It truly is fascinating stuff.


The Microbiome and the Tryptophan/Serotonin Pathway

Tryptophan is an essential amino acid that is required for the synthesis of serotonin in the brain and gut, and melatonin in the pineal gland.5 The former is a neurotransmitter that regulates mood and is often referred to as the “happy chemical,” while the latter is a hormone that regulates sleep. Remarkably, 90% of serotonin (5-HT) produced is in the gut, and its synthesis is directly impacted by the state of the microbiome; thus, confirming that your digestion really does affect your mood!

Although tryptophan is most commonly known for its role as the precursor for serotonin, the majority is actually used via an alternative route used in the kynurenine pathway.2 This is highly significant because the microbiota appears to control the tryptophan metabolism through this pathway. Moreover, chronic stress and infection can further shunt tryptophan toward the kynurenic pathway and thereby lowers 5-HT synthesis,5 further confirming the role the microbiome plays in the stress response and inflammation which affects your mood. Although complex to say the least, it is remarkable how intricately connected the GB axis is!


Dietary Considerations for Mood

It is now clear how important a healthy microbiome is for your mood and cognitive function, and although one can attain and maintain a healthy microbiome, proper nutrition is also needed for the synthesis of serotonin. Although tryptophan is key to making serotonin, its metabolism is a bit complicated, so effort needs to be made when optimizing tryptophan through diet.

Now, herein lies the tryptophan rub. Like it or not, you need to eat complex carbohydrates, not high-protein for it to be successfully absorbed and converted to serotonin. Some of you may be having a mini heart attack while reading this, but before you do, remember last month’s article on resistant starch. We learned about the importance of complex, unrefined carbohydrates for the health of the microbiome, so it should not come as a surprise they are needed in the tryptophan metabolism and here is why.

Proteins are made up of amino acids, but tryptophan is the least concentrated of the bunch. To further complicate things, the other amino acids are also larger so when tryptophan enters the brain, they outcompete it for uptake.

However, when a complex carbohydrate is eaten–ideally a high resistant starch–it increases brain tryptophan because insulin levels will rise. This causes uptake of the larger amino acids into muscles allowing tryptophan to be taken up by the brain. Again, bear in mind that complex carbohydrates are not highly digestible, refined carbohydrates. As such, they take longer to digest; therefore, create a much slower release of insulin. A prebiotic or resistant starch food will also feed the good bacteria in your gut further ensuring a healthy glucose metabolism. It is definitely a win-win!

So how does one not only eat for their gut health, but their brain? If you eat plant-based this is a little more simple, seeing plant proteins are unique in that they are both complex carbohydrates and proteins. For example, chickpeas and black beans are rich sources of tryptophan and high in resistant starch.

The best rule of thumb is to eat from the resistant

If you consume animal proteins, stick to lean, high-quality ones such as turkey, chicken and salmon. Aim to then snack on complex carbohydrates, ideally high resistant starch foods every day. This way, you are getting all the right stuff to ensure maximum uptake of tryptophan in the brain. Find more information on tryptophan here.


Specific Nutrients for Mood and Stress

Another important consideration are B vitamins. They are critical to numerous processes in the body—especially regarding the central nervous system. B6, B9, and B12 are of particular importance seeing they are required for serotonin synthesis. B vitamins are water-soluble; they are not stored in the body and are readily depleted in times of stress. They also need to be in their active, bioavailable forms and in specific doses, so add a high-quality, well-researched B complex to your routine.

Other critical nutrients to consider are magnesium, vitamin D and omega-3 fatty acids. Magnesium—the “miracle mineral” is involved in over 300 chemical reactions, but is specifically required for serotonin synthesis and regulating the stress response. Vitamin D and omega-3 fatty acids are also involved in the synthesis of serotonin. Research has confirmed that magnesium is required for vitamin D absorption; thus, it is clear how interconnected even these nutrient profiles are.


Other Ways to Increase Serotonin and Manage Cortisol

Some simple lifestyle factors greatly impact serotonin and manage cortisol. The first is good old fashion exercise. Several lines of research suggest that exercise increases serotonin function in the human brain.6 There is an increase in brain tryptophan post-exercise—especially if one is brought to fatigue. Even better, studies have shown that exercise improves microbiome health by shifting gut bacteria towards the growth of beneficial bacterial strains.3

A second option is increasing your exposure to sunlight. It is no surprise how much sunlight affects mood and the role vitamin D plays in serotonin clarifies why. Light is measured in lux and studies have shown that the mood lowering effect of acute tryptophan depletion in healthy subjects is completely blocked by light at 3000 lux. Even on a cloudy day, the light outside can be greater than 1000 lux, a level normally never achieved indoors,6 so get outside! Those of us here in the Great White North have issues with sunlight exposure in the winter months; therefore, investing in a specialized high lux light may be a good idea.

The third option is deep breathing, yoga and meditation. Just ten deep breaths can effectively reduce stress, cortisol and lower heart rate; thus, positively impacting the microbiome, which in turn influences serotonin synthesis. So breathe like your life depends on it, cause it really does!

Gut Disruptors, Dysbiosis and Inflammation

It is common knowledge that antibiotics significantly disrupt the microbiome because they do not differentiate between beneficial vs. harmful bacteria. The good strains are then wiped out which wreaks havoc on the gut. This extreme imbalance causes immune cells to be further activated, leading to gut inflammation and increased permeability of the intestinal barrier. These looser junctions (leaky gut) then allow toxins and other harmful substances to enter into the circulation.

This then activates the release of proinflammatory cytokines causing inflammation in the brain and the central nervous system. Yes, you read that right, dysbiosis causes inflammation in the brain, which then drives mood disturbances and other psychiatric and central nervous system disorders. Gut inflammation does not just spread to the brain, it spreads to the entire body. Lastly, it has been stated that inflammation is the root of most diseases and this insight into the GB axis shows us how, further confirming that your gut truly is the wellspring of your health—treat it right!

Gut disruptors don’t just come in the form of antibiotics, they are commonly used medications, cannabis and alcohol. The irony here is that the majority of these substances are used to treat specific symptoms, but in fact, they actually drive the symptoms they are designed to treat because of their impact on the microbiome.

The most bewildering of all the disruptors are selective serotonin reuptake inhibitors (SSRIs) which are used in the treatment of anxiety and major depressive disorder. They don’t synthesize serotonin, but work to redistribute it between synapses. This seems fairly benign and logical; however, there is considerable evidence of their antimicrobial action, meaning they will disrupt the serotonin metabolism. Further, seeing SSRIs are usually taken for long periods, at high doses and absorb very slowly, their impact as microbiome disruptors are very significant. It really is a catch 22 and may leave some in a vicious cycle of symptomatology that never breaks. This is not to say that SSRIs are not useful to many people, and don’t have their place in the treatment of the aforementioned conditions. However, due to mounting evidence, it is clear that the microbiome needs to be considered when prescribing these medications.

Other commonly used gut disruptors are nonsteroidal anti-inflammatory drugs (NSAIDs), proton-pump inhibitors (PPIs) and opioids. Let’s not forget Mary Jane and her BFF Jack Daniels. They are mainstays for many, but powerful gut disruptors; therefore, make diligent moderation your goal when you want to hang out with them.


Replenishing the Microbiome and Supporting the Gut-Brain Axis

Now, I imagine this particular scuba session has left some of you feeling overwhelmed, seeing as it appears that everything impacts your microbiome. So what is one left to do when dealing with mood disorders or requires prescription medications?

Well, the simple answer is getting back to basics by seriously cleaning up your diet. Whether you lean toward an animal-centric or plant-centric diet, be sure it is based on whole foods that are ideally organic, or free of pesticides and herbicides, it’s unprocessed, unrefined and non-industrialized. Simply put, cut out all the fake, chemically-laden stuff! Fruits and vegetables should be front and centre no matter what diet you follow and always accompanied by fermented foods, prebiotic fiber, resistant starch and a low glycemic approach. As stated in the previous article, eat what makes you feel good, limit portions where needed and start slow when adding in any new foods—especially resistant starch.

If possible, consider working with our registered holistic nutritionist to help to get your diet and gut back on track. However, if you are ready to entirely transform your life and finally get to the root of your issues, then it may be time to consider booking in with one of NutriChem’s team of experts. They specialize in microbiome mapping, and sit on the Canadian Deprescribing Committee and can help you safely and effectively come off your prescription medications if desired.

*This article is not intended to represent medical advice. Please contact a qualified health practitioner if you want to use any natural health products for specific health conditions. Further, always consult your physician before adjusting or coming off of any prescription medications.


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Abigail S McGovern, Adam S Hamlin. “A Review of the Antimicrobial Side of Antidepressants and Its Putative Implications on the Gut Microbiome – Abigail S McGovern, Adam S Hamlin, Gal Winter, 2019.” SAGE Journals. 26 Sept. 2019. Web. 25 Mar. 2021.

Patrick, Rhonda P., and Bruce N. Ames. “Vitamin D and the Omega-3 Fatty Acids Control Serotonin Synthesis and Action, Part 2: Relevance for ADHD, Bipolar Disorder, Schizophrenia, and Impulsive Behavior.” FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology. U.S. National Library of Medicine, 24 Feb. 2015. Web. 25 Mar. 2021.

Cuciureanu, Magdalena D. “Magnesium and Stress.” Magnesium in the Central Nervous System [Internet]. U.S. National Library of Medicine, Jan. 2011. Web. 25 Mar. 2021.

Perreau-Linck, Elisabeth, Mario Beauregard, Paul Gravel, Vincent Paquette, Jean-Paul Soucy, Mirko Diksic, and Chawki Benkelfat. “In Vivo Measurements of Brain Trapping of C-labelled Alpha-methyl-L-tryptophan during Acute Changes in Mood States.” Journal of Psychiatry & Neuroscience: JPN. Canadian Medical Association, Nov. 2007. Web. 25 Mar. 2021.

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Dr. Emma Pollon-Macleod
Dr. Emma Pollon-Macleod, B.Sc., N.D.

Dr. Emma is a passionate advocate for natural, holistic healthcare, making it her mission to determine the root cause of illness. Her background in biochemistry allows her to navigate complex health conditions and provide realistic and effective treatment plans for her patients. Dr. Emma’s naturopathic practice has a focus on hormonal health, including genitourinary and pelvic health and complex allergy conditions, such as mast cell activation syndrome.

Areas of special interest:

  • Allergic Conditions (MCAS, idiopathic urticaria, etc.)
  • Hormonal Health
  • Digestive Health
  • Pelvic health (Interstitial cystitis, chronic UTIs)