Your Microbiome & Your Mood

Have you ever noticed that what you eat impacts your mood? Have you felt worse after binging on junk food or after a night of drinking? There is compelling research suggesting that it may not be just the guilt talking – your microbiome may be contributing in a large way to the conversation.

What is the microbiome?

There are 10 to 100-trillion symbiotic microbes of various species existing in and around the human body, collectively referred to as the microbiome 25. These friendly microbes outnumber your own human cells and have recently become popularized for the growing body of evidence detailing the vast impacts they have on human physiology and behaviour.


We acquire our microbiome and much of our immunity as newborns via the birth canal and through breastfeeding 23. These important contacts seed the microbiome. In healthy individuals, this proliferates to confer many different essential functions that help us to thrive. From as early as birth we are impacted by the microbiome – the presence, quality, and diversity, or lack of, which determines and contributes to the development of our digestive tract, as well as our nervous and immune systems 8, 18, 20.

The microbes in your intestines make vitamins, amino acids, hormones, neurotransmitters and other signalling molecules that impact the way your brain and body function 5, 21. They also produce short chain fatty acids as byproducts that your intestinal cells use for energy, which contributes to healthy gut function 21.

These bugs live in our digestive tract and survive off the foods that we eat. Just like any other living organism, their health (and therefore ours) depends on consuming a healthy diet. It has been shown that dietary changes (e.g. from animal-based to plant-based), as well as any significant systemic stress and inflammation can alter the composition (i.e. diversity and abundance of species) of your microbiome within just 24 hours 21.

How does this affect your body?

The microbiome positively contributes to our immune system by modulating innate and adaptive immune responses, and by influencing immune cell counts and function 17. Having a sufficient population of good bacteria also serves as a direct defence system against pathogenic microorganisms 17 by occupying your intestinal territory and preferentially consuming nutrients so that it’s less likely for pathogens to successfully invade.

Altered microbiome composition has been associated with many conditions, such as inflammatory bowel disease (IBD), psoriasis, atopic dermatitis, autoimmune arthritis,  type 2 diabetes, obesity, and atherosclerosis 21. This is not surprising given the significant role these organisms have in regulating metabolism and immunity. In fact, researchers are finding that the microbiome composition in a given pathology seem to have a different complement of microbes associated with it. For example, an IBD microbiome has less diversity (fewer species of healthy microbes), and lower numbers of good bacterial species. Therefore, it has lower short chain fatty acid production 21. Short chain fatty acids (SCFAs) are essential to the health of your intestinal cells and are also thought to be anti-inflammatory in the gut 21.

Studies in mice have shown that transplanting gut microbes from mice with certain conditions can induce these conditions in the mice they were transferred to. Turnbaugh et al. transferred microbes from phenotypically obese mice to non-obese mice, which induced obesity in the previously non-obese mice 24. Their research also found that the obese-phenotype microbiome in these mice had increased capacity to harvest energy from the host diet 24, meaning the microbes in the obese mice extracted more calories from their diet than the non-obese microbe population. This lead to a comparatively higher caloric intake over time, thus contributing to the obesity 24.

The Microbiome’s Effect on Mood & Behaviour

Gut microbes relay messages to the brain via various direct and indirect mechanisms – bacterial metabolites, metabolic precursors, immune signalling, vagus nerve signalling, and Hypothalamic-Pituitary-Adrenal axis activation 6, 20. It is via these mechanisms that neurodevelopment or neurodegeneration are influenced 20. A significant portion of the microbiome influence on the brain comes via the gut-brain axis – a bi-directional pathway connecting the nervous system in your digestive tract to the central nervous system (your brain) 6, 20. As shown in the graphic below, your gut and your brain communicate directly via nerves that transmit different signals and molecules, which can have a profound effect both ways to both systems 15.

Gut-Brain Connection
Photo credit: //

Considering the gut-brain axis and the physical manifestations that different microbiome composition can produce, it should be no surprise that there are mental/emotional implications as well. Many psychiatric and neurological pathologies have gastrointestinal co-morbidities, including schizophrenia, autism, neurodegenerative diseases, anxiety, and depression 18. As noted above, different pathologies have different microbiome composition. This extends to mood and neurodegenerative disorders, such as major depressive disorder, schizophrenia, Parkinson’s disease, and autism spectrum disorder 5, 12, 20. There is also data suggesting that alterations in the microbiome in addictions (eg. alcohol, cocaine) may be associated with substance cravings and increased risk of developing associated psychiatric disorders, such as anxiety and depression 10, 13.

In various animal studies, researchers were able to observe differences in neurodevelopment between mice who inherited or were colonized with an adequate microbiome and mice who were given antibiotics and a sterile environment (to eliminate the microbiome). The microbially sterile mice were prone to neurologic and immune deficits that in some cases could be reversed given the proper support, including colonization with proper microbes 5, 8, 13, 20, 24. I nor the researchers in these studies are saying that we can cure these conditions with a probiotic or microbial transplant (though research is exploring this possibility), but rather that it is becoming increasingly important to recognize the significance of the connection between the health of your gut, microbiome, and brain.

What influences the health of our microbiome?

Many different lifestyle and dietary factors affect the health of our microbiome. Being situated in the digestive tract, diet is a big influence. The research surrounding nutrition and the microbiome are constantly evolving, however there is some overlap of recommendations in both areas. Consuming a more plant-based diet was more beneficial than one high in animal protein 21. Plant-based diets have been found to favour microbes that produce SCFAs, which provide energy to the intestinal cells and are thought to have an anti-inflammatory effect on the gut as well 21. In line with this, diets higher in animal protein led to less SCFA-producing bugs, and were found to be associated with higher inflammation and inflammatory bowel disease 21. Similarly, mouse studies demonstrated that diets high in saturated fats increased proliferation of microbes that promoted metabolic inflammation and insulin resistance 21. In terms of carbohydrates, natural sugars were shown to be beneficial by feeding the good microbes, while consumption of artificial sweeteners resulted in higher numbers of pathogenic microbes compared to beneficial microbes in mouse microbiome studies 21.

Non-digestible carbohydrates (fibre) selectively stimulate the proliferation of certain microbes 21. Specific forms of fibres are known as prebiotics (food for the microbes), and include soybeans, inulin, unrefined grains, and certain undigestible sugars 21. High-fibre diets are positively correlated with an abundant, healthy microbiome, and beneficial effects on immune and metabolic function 21.

Different diets impact the microbiome relative to their composition. The typical western diet – high in animal proteins and fat, but low in fibre – was associated with a less abundant and less diverse microbiome 21. Gluten-free diets had decreased numbers of microbes overall, leading to an increased population of opportunistic pathogens 21. The Mediterranean diet (a wide variety of whole foods, rich in antioxidants, abundant consumption of plant-based foods, moderate animal protein consumption, and inclusion of healthy fats) is known for its benefits on cardiovascular health, improving obesity, lipid profiles, and lowering inflammation, and was found to be most beneficial to microbiome composition 21.

Last but not least – going straight to the source – probiotics! The direct addition of  beneficial microbial species (probiotics) to your digestive tract through capsules, powders, fermented foods & beverages (e.g. kimchi, sauerkraut, yogurt, kombucha), or via fecal microbial transplant can be an efficient way to support your microbiome while you implement lifestyle changes for long-term health. The benefits of probiotics are many and may include the alleviation of digestive symptoms, reduction of pathogenic species within the gut, reduced ‘bad’ cholesterol (LDL), increased ‘good’ cholesterol (HDL), improved insulin sensitivity, and decreased inflammation 21.

Probiotics used to benefit mood and cognition have been coined “psychobiotics,” and are a burgeoning new area of interest in research.  A study by Tillisch et al. used brain scans (functional magnetic resonance imaging) to demonstrate the ability of probiotics to alter brain activity in areas associated with processing emotion and sensation, and to reduce negative thinking associated with sad mood 6, 17, 18, 22. While most studies indicate that further research in this area is needed, associations between specific strains of microbial species and their benefits on various conditions are rapidly emerging 8, 18, 19.

A healthy lifestyle goes a long way in supporting your microbiome, and healthy eating is just one part of it. As mentioned earlier, dietary changes, significant systemic stress, and inflammation can alter your microbiome within just 24 hours. There are many different types of stress – physical, mental and emotional – that can lead to physiologic changes that can alter the microbiome. Practicing stress management through self-care, meditation, social connection, thoughtful schedule planning, getting adequate sleep, and setting appropriate boundaries with people and responsibilities will help you be more resilient in dealing with stress. The better you are at managing stress, the less likely it will spill over into added physical or mood-related symptoms.

If you’re having trouble managing your stress, sleep, mood, or digestion, we’re here to help. Call the clinic (604) 670-0590 or book online here for an appointment.

New to Tandem or naturopathic medicine in general? We offer free 15 minute meet-and-greets so you can decide if we’re the right fit. If not, we’re happy to direct you to one of our colleagues who might be.

Wishing you health, wealth, and every happiness,

Dr. Jacalyn Sieben, ND




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