In today’s post we will be diving deep into what is currently known about the gut microbiota, the relationship between the gut microbiota and our mental health, and the role of nutrition (including prebiotics and probiotics).

What is the Gut Microbiota?

The gut microbiota describes the microorganisms – including bacteria, archaea, eukaryotes, and viruses – that call our intestines home. (1) Collections of microorganisms, or microbiotas, also exist in and on other areas of our body – such as our skin, mouths, and respiratory systems. (1,2,3)

Similar to our fingerprints, no two microbiotas are the same. (2,4) The collection of microorganisms that inhabit our gut vary depending on a number of factors – some of which are out of our control, such as genetics, aging, or vaginal vs. C-section birth, while others have the potential to be changed, such as our diet, medications, environment, or overall lifestyle. (1,3,4) The gut microbiota that is formed in childhood remains relatively stable throughout an individual’s lifetime but may change with age, disease, antibiotic use, (1,4) or modifications in the diet. (5)

Mental Health & the Gut Microbiota

The term “microbiota-gut-brain axis” is used to describe the symbiotic relationship and communication between our gut microbiota and our brain. (2,3,4) Our understanding of this connection is very much in its infancy, but research suggests the microbiota-gut-brain axis is involved in a number of disease processes, including anxiety, stress, psychiatric disorders, neurodegenerative disorders, addiction, and IBS, among others. (2) This may likely be related to dysbiosis – an imbalance in the composition or function of the gut microbiota. (6)

For instance, one study investigated the relationship between the composition of an individual’s gut microbiota, quality of life, and depression. (7) Researchers found that two species of bacteria that are associated with greater quality of life were consistently lower in individuals with depression who were not receiving antidepressants. (7) While we cannot assume that a deficiency in certain microbes is the cause of mental illnesses like depression, it does suggest that there is an association – it is possible that depression itself, or its impact on an individual (such as changes in diet, lifestyle, exercise, etc.), may impact the composition of the gut microbiota, (6,5,7) and lead to dysbiosis.

Further, changes in the microbiota have been found in rodent and some human studies to play a role in regulating areas of the brain that are involved in fear (which is an element of both stress and anxiety), (2) and a recent review highlighted a possible relationship between the presence or lack of certain microbes and generalized anxiety disorder or feelings of stress. (8) 

So, What Role Does Nutrition Play?


Prebiotics include certain non-digestible carbohydrates, primarily fructo-oligosaccharides (FOS) and galacto-oligosaccharides (GOS) (see list below for examples of prebiotic sources). (9.10) These compounds are difficult for the human body to breakdown, but the microorganisms within the gastrointestinal system can metabolize them through a process called fermentation. (6,9) It is through this process that prebiotics are broken down and short-chain fatty acids (SCFAs) are produced. (6,9)

SCFAs have been found to serve as an energy source for microbial growth, but they also benefit the human body by supporting processes such as lipid metabolism, immune function, and appetite regulation. (9) An individual’s response to prebiotics can vary greatly depending on the type and amount of prebiotic consumed, and the type of bacteria that inhabit their gut – certain bacteria may make efficient use of a particular prebiotic, so fermentation of this prebiotic may be lower in individuals who have lower levels of this bacteria. (9) Different bacteria use or prefer different forms of prebiotics, making it beneficial to include a variety of different prebiotics within one’s diet – this can help to support a diverse collection of microorganisms, which may be considered one of the hallmarks of a healthy microbiota. (6,9,10)

Early research also suggests that prebiotics may influence mental health, including stress and anxiety, but the mechanisms behind this relationship are not yet understood. (2)

Some research suggests that diets high in processed sugars, artificial sweeteners, and saturated fat, and low in fibre (and prebiotics), may negatively impact the gut microbiota and result in damage to the cells that line the intestines. (5) Known as “leaky gut,” this condition is also associated with an ‘unhealthy’ gut microbiome. (5) Meanwhile, diets higher in fibre (including prebiotics) and unsaturated fats have been shown to support a healthy gut microbiota. (5)

Sources of Prebiotics: Prebiotics are found primarily in fruits, vegetables, and whole grains. Some specific examples include bananas, onions, garlic, asparagus, beans, Jerusalem artichoke, sugar beet, chicory root, wheat, barley, rye, tomato, soybean, seaweed, honey, cows’ milk, and breastmilk. (11)


Despite having a very similar name, probiotics are quite different from prebiotics – probiotics are live microorganisms that may have beneficial health effects if consumed in adequate amounts. (6,12,13) The specific effects of probiotics vary depending on the strain consumed – for example, certain strains may suppress the growth of pathogenic microorganisms, (13,14) produce beneficial by-products, (13) or play a role in vitamin synthesis. (13)

For a food or supplement to be considered a source of probiotics, it must provide a specific number of bacteria per serving from an accepted bacterial species. (12) Accepted bacterial strains have been studied and are likely to have a beneficial effect on human health and the gut microbiota. (12) Further, probiotics comprised of a specific bacterial strain can provide some relief in certain diseases or conditions (such as IBS, IBD, antibiotic-associated diarrhea, stress, and depression), and may be used in combination with standard treatments (2,15) – therefore, working with a health care professional to determine which probiotic may be most appropriate for you is recommended. Currently there is no recommended daily intake for probiotics for otherwise healthy individuals, however, some research suggests including probiotic sources on a regular basis may support a healthy gut microbiota, which in turn may benefit overall health. (16)

Only certain foods thought to be probiotics have been found to contain live microorganisms that actually survive travel through the gastrointestinal system after being consumed. (13) Most fermented foods, such as cheese, kimchi, pickles, kombucha, sauerkraut, miso, and raw apple cider vinegar, do not contain proven probiotic microorganisms. (13) However, there is evidence to support the use of yogurt and fermented milk products as a source of specific probiotic strains, which may play a role in the management of certain conditions. (15)

Probiotics are also available in the form of supplements, however, not all products on the market are created equal. Probiotics may contain one or more bacterial strains, and in varying amounts. (13) However, only specific probiotic strains in specific quantities have been researched and shown to have a beneficial effect on health or disease. (13) Working with a health care professional, such as a registered dietitian, to determine if taking supplemental probiotics would be beneficial for you is recommended.

A recent review of the literature concluded that current research supports the use of probiotics in the treatment of symptoms of depression, but there is insufficient evidence to draw conclusions regarding the role of probiotics in anxiety treatment. (14) Further research is needed to truly understand the role that probiotics may play in other mental illnesses, or in support of overall mental wellbeing and stress management.

If you’re wondering whether adding probiotics is right for you, or if changes to your diet may help in managing certain health conditions, a Registered Dietitian at Nutrition Assessment Clinic can help.

Written by Mikaela Horton, BASc, MHSc, RD for


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