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What is The Gut Microbiome's Role in Mental Health Disorders?

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What is The Gut Microbiome's Role in Mental Health Disorders?

The gut plays an incredible role in influencing all aspects of our health. From digesting and metabolizing our food to synthesizing vitamins, hormones, and neurotransmitters, the gut helps regulate many of the body's functions integral to overall health. It even supports inflammation, immunity, and detoxification. Perhaps most exciting and empowering, however, is the role of the gut and the microbiome in our overall mood and mental health. In fact, the gut is often referred to as the "second brain."

The World Health Organization (WHO) has identified mental health as an epidemic of the 21st century, making this connection particularly interesting in the functional medicine world. While many factors are involved in the etiology of mental and physical health, significant research indicates a direct relationship between gut health - primarily the composition of the microbiome - and mental health.


What is The Gut Microbiome?

Currently, trillions of bacteria reside in the gut, collectively called the microbiome. The gut microbiome includes about 100 trillion microorganisms, including bacteria, viruses, fungi, archaea, and eukaryotic organisms that all live synergistically. Some pathogenic (harmful) and opportunistic bacteria exist, even in healthy guts. But, the diversity and balance within the microbiome matter the most regarding overall physical and mental health.  

Emerging research also indicates that each strain of bacteria within our microbiome contains a genome comprising thousands of genes. Therefore, by supporting our microbiome health, we have the power to influence gene expression in favorable ways, ultimately benefiting our mental health.

What is Mental Health?

Mental health is characterized as a subset of symptoms pertaining to overall functioning, mood, and well-being. Our mental health impacts how we feel, think, and behave.

Millions of individuals worldwide struggle with their mental health. It is suggested that 1 in 5 American adults experience a mental health disorder that can significantly impede one's functioning, well-being, and overall quality of life, including their health.

The etiology of mental health is multifaceted. It includes our unique biochemical makeup, our experiences, such as adverse childhood experiences and trauma, and our genetic predispositions. Nutrition and lifestyle can help to modulate and optimize different processes in the body that influence how we feel physically and mentally. The health of our gut microbiome is an example of this.

What is The Gut Microbiome's Role in Mental Health Disorders?

Several neurotransmitters, hormones, and vitamins vital for mood health are synthesized in the gut. Over 90% of Serotonin, an important neurotransmitter relative to mood, is synthesized in the gut. GABA, an inhibitory, calming, and uplifting neurotransmitter, is produced in the gut, as is Dopamine, a neurotransmitter involved in reward and mood.

The gut microbiome significantly affects gastrointestinal motility, digestion, elimination, and absorption of nutrients. It also influences our hormones, metabolic health, nervous system functioning, and levels of inflammation in the body, all of which contribute to our mental health.

The gut microbiome, the brain, and the rest of the body are always in communication through neural pathways controlled by our nervous, endocrine, and immune systems. The gut-brain axis describes this bidirectional communication via the vagus nerve between the body and the brain.

The vagus nerve is the longest cranial nerve in the body and represents a main component of the parasympathetic nervous system, helping to regulate mood, immunity, digestion, and heart rate. The vagus nerve relays information about the physiological and psychological state of the body to the brain via afferent fibers. This is termed bottom-up communication, and it represents 80% of the communication in the body.  

Comorbidities between mental health and gut health conditions are well documented in the literature. Research suggests there are patterns of altered gut microbiota composition in those with various mental health conditions. For example, this systematic review found that there were marked differences in gut microbiota composition in those with Major Depressive Disorder (MDD), Bipolar Disorder, and Schizophrenia in comparison to healthy controls. Further research supports this in multiple studies, such as in those with Generalized Anxiety Disorder (GAD) Obsessive Compulsive Disorder (OCD), and even with evidence for addiction.

Symptoms of Unbalanced Gut Microbiome

Common symptoms of an unbalanced gut microbiome are vast, including anxiety, depression, brain fog, fatigue, metabolic issues, hormonal imbalances, difficulty concentrating, irritability, compromised immunity, poor detox capacity, and fluctuations in mood. An unbalanced microbiome also manifests as signs of compromised digestion and inflammation. This can affect our body's ability to digest, efficiently absorb and assimilate nutrients, and detoxify harmful substances and waste that could impede our health and mental health.

Furthermore, problems with sleep may arise due to an unbalanced gut microbiome which can further exacerbate mental health symptoms. Also, when our gut microbiome is out of balance, we may be more prone to infections, as 70-80% of our immune system is housed in the gut.

An unbalanced gut microbiome can further exacerbate underlying nutritional deficiencies, which can wreak havoc on our mental health as nutrition is significant to our mental health.

What Causes an Unbalanced Gut Microbiome?

There are several potential causes for an unbalanced gut microbiome. Below are some of the most evident causes:

Genes and Early Environment

Evidence suggests that our gut microbiome begins getting shaped in terms of its composition beginning as early as we are born. Vaginal births have been found to expose us to more diverse gut bacteria, helping to set the foundation for a healthy and balanced microbiome. Being breastfed over bottle-fed also exposes us to a diverse range of healthy microbiota.  


Chronic stress over time can cause imbalances in the gut microbiome leading to dysbiosis. Stress can also reduce stomach acid in the gut, impeding diversity in the microbiome.

Toxin Exposure

Toxin exposure from our environment can cause oxidative stress in the body, negatively impacting gut functioning and our mental health. This could include exposure to mold, toxic metals, or lifestyle factors such as alcohol consumption or smoking.

Dysbiosis From Antibiotics & Poor Nutrition

While there are times when antibiotics are warranted, continued courses of antibiotics can disrupt the balance of bacteria in the gut. Antibiotics have been found to alter gut the barrier, induce dysbiosis, and increase inflammation and cortisol; all of which can further impede the health of our gut microbiome and our mental health.

The foods we eat directly affect the composition of the gut microbiome. Processed foods, refined carbs, and alcohol, as well as foods and drinks high in sugar or additives, can compromise the balance of the gut microbiome, its integrity, and its functioning. These foods are also depleted of nutrition. Whereas eating a diverse, nutrient-dense whole-food diet can have the opposite effect.

Inflammatory foods (such as gluten and often dairy) can also contribute to an unbalanced microbiome, as well as foods that may cause irritation to the gut lining or that the body has sensitivities to.

Thyroid Function & Hormonal Imbalance

Thyroid function is imperative for energy and metabolism, as well as mood. When our thyroid isn't functioning as it should, this can also cause imbalances in our microbiome and gut health. Chronic stress can cause alterations and dysregulation in the HPA axis, leading to hormonal imbalances, which can further wreak havoc on our mental health and gut health.

Functional Medicine Labs to Test for Root Cause of Unbalanced Gut Microbiome

Functional medicine labs help examine the underlying causes of an unbalanced gut microbiome resulting in mental health disorders. Below are some great examples of labs run by practitioners:

3 x 4 Genetics Test + Blueprint Report

This comprehensive test gives us valuable insight into 36 measures of our health relative to inflammation, metabolism, methylation, detoxification, hormones, and mood. This improves knowledge of how one's body systems function based on their unique genetic make-up, what conditions they may be more susceptible to, and areas that could use more focused support.


This test can rule out any hormonal imbalances and examines the function of the HPA axis and stress hormones, which can affect the gut microbiome and mental health.


This Environmental Toxins test is a urine test that assesses for toxic exposure from one's environment. This can give insight into whether toxins are affecting the gut or mental health.


This test is a comprehensive stool analysis that assesses gut DNA from a single stool sample, providing valuable insights into our microbiome diversity and overall health. Our gut bacteria have their own DNA or genome and express those genes based on their own environment, which can be greatly influenced by nutrition and lifestyle factors.

Micronutrient Testing

When there is a dysfunctional gut affecting the absorption of nutrients, deficiencies are likely to occur. Nutritional deficiencies can contribute to and exacerbate mental health symptoms. Ensuring one is sufficient in all the vitamins and minerals important for mental health is therefore important. The Micronutrient test analyzes many nutrients that one may be deficient in.

Food Allergies/Sensitivities

This test is helpful as it can determine if an intolerance to gluten or other foods is evident, which can further contribute to symptoms of inflammation, exacerbate nutritional deficiencies, and alter gut bacteria balance.

Functional Medicine Treatment for Gut Health & Mental Health

A functional medicine approach to gut and mental health addresses the underlying contributing causes of these symptoms.

Gut Health Balance for Mental Health

A common and effective gut healing protocol is the "5 R Protocol" - Remove, Replace, Reinoculate, Repair, and Rebalance. This consists of Removing what can disrupt gut functioning (this includes an individual's food sensitivities); Replacing with digestive enzymes, HCL, or bile that one may be deficient in; Reinoculating with diverse nutrient-dense and probiotic-rich foods;  Repairing with things like L-Glutamine and zinc to repair the gut lining and inflammation; and Rebalancing, referring to supporting balance between body and mind, which greatly impacts gut health.

Environmental and Lifestyle Factors to Address for Mental Health

Assess the quality and purity of your air and water and any specific toxin exposures that were present in test results. Being mindful of alcohol intake is also vital, as alcohol can compromise the gut lining, leading to inflammation and contributing to less beneficial gut microbiota.

Hydration, rest, and movement are also imperative to mental and physical health. Movement can benefit your gut microbiome and mood as exercise releases feel-good endorphins. Sleep is imperative for a balanced gut microbiome and mental health. Also, microbiome health is correlated with adequate sleep. Sleep helps to detoxify and restore the body and mind, helping to promote healthy gut functioning, including microbiota balance.

Nutrition for Mental Health

The Microbiome diet is an anti-inflammatory, nutrient-dense, and probiotic-rich way of eating. It helps to rebalance the microbiome, thereby healing gut and mental health. This whole foods diet is also rich in phytonutrients, polyphenols, prebiotics, fiber, and omega 3s, which are known for powerful anti-inflammatory and positive mental health properties. Refraining from processed foods high in sugars and refined carbs is also important, as these foods wreak havoc on the gut microbiome.

Gluten and dairy should also be avoided during healing since these are inflammatory foods. Individual food sensitivities should also be avoided while healing.

Proteins are made of amino acids, which are essential for building neurotransmitters. Adequate protein intake is, therefore, key when eating for mental health. Leafy greens such as spinach, avocado, and kale are loaded with antioxidants. They are great sources of folate, which have essential roles in terms of methylation, a process imperative for neurotransmitter production, hormone regulation, gut functioning, digestion, and detoxification. Folate also plays a significant role in serotonin synthesis, which is important for our mood.

Other great food additions include good quality dark chocolate (the higher the cocoa percentage, the better), which has been shown to increase Brain-Derived Neurotrophic Factor (BDNF), decrease inflammation, and help to increase blood flow to the brain, and seafood, which provides omega 3s, protein, B vitamins, and zinc, which helps to modulate neurotransmitter, hormonal, and gut functioning.

Vitamins for Mental Health

Many vitamins and minerals are cofactors to many biological processes, like neurotransmitters needed for a healthy mood and outlook. Therefore, it is important to include vitamin-rich foods.

B vitamins are essential to mental health and gut functioning. While many B vitamins are essential for energy, they also serve as important cofactors for many neurotransmitters imperative for mental and gut health. Several B vitamins also aid in methylation, a significant process to the body's overall functioning.

For example, Niacin (vitamin B3) increases tryptophan, an amino acid vital for the production of serotonin. Sources include poultry, salmon, and leafy vegetables. Pyridoxine (vitamin B6) is a cofactor for Dopamine, GABA, Melatonin, and Serotonin, all vital for mood and gut health. Foods rich in B6 include fish, poultry, nuts, avocados, bananas, and legumes. Folate (vitamin B9) is integral to mental health, particularly in methylation and serotonin neurotransmission. Sources of folate include leafy greens, beans, eggs, grass-fed meat, and poultry. Vitamin B12 serves as a cofactor for serotonin and dopamine. It also has a significant role in nervous system health and methylation. Sources of B12 include animal products, poultry, and shellfish.

Vitamins C and E are antioxidants that help combat stress, support nerve cell function, and sufficient detox. Deficiencies in these antioxidants reduce levels of tryptophan, which is needed for serotonin production.

Supplements & Herbs for Mental Health

While it is always recommended to get most of your nutrition from foods, several supplements and herbs support the gut microbiome and mental health. It is important to consult with your physician before starting a new supplement regimen. Bio-individuality is an important factor in terms of determining optimal dosage.

In addition to probiotics obtained from food, psychobiotics are defined as probiotics that have mental health benefits to the host when consumed. Several strains of probiotics have been suggested to reduce symptoms of anxiety. The mechanisms in which this occurs is thought to be through the synthesis of important neurotransmitters for mood, such as GABA and serotonin, regulation of inflammation, and improving the stress response through exerting favorable effects on the HPA Axis and stress hormones.

Omega 3 fatty acids can also be obtained through food. However, a recent meta-analysis showed the beneficial effects of Omega 3 supplementation on participants with Major Depressive Disorder (MDD).

Magnesium assists with over 200 enzymatic reactions in the body, influencing how we feel. Magnesium has a role in nervous system health as well as depression, inflammation, and digestive health.

Curcumin (turmeric) helps with inflammation and positively affects our gut microbiome and mental health. In this double-blind, crossover trial study, curcumin decreased symptoms of anxiety.

CBD has been found to have anti-inflammatory properties in the body and brain, helping to support digestion, microbiome health, and mood.  

Complementary and Alternative Medicine for Mental Health

Practices for regulating stress, such as mindfulness, deep breathing, connecting with others, and spending time in nature, are a great place to start and truly foundational for health. Also, being aware of our diet's connection to our gut microbiome and the connection between a well-balanced microbiome and our mental health can be empowering. Here are some other CAM practices that can be beneficial for gut and mental health:

Yoga has been found to increase vagal tone, supporting gut functioning, nervous system health, and mental health. Chiropractic treatment has also been found to stimulate the vagus nerve, benefiting depression, increasing relaxation, and releasing neurotrophins such as BDNF, which promote neuroplasticity and anti-inflammatory benefits.

Meditation has promising benefits on gut and mental health as it supports parasympathetic nervous system dominance in the body and mind.

Cold exposure has been researched for gut functioning, balance, and mental health, specifically impacting our neurotransmitters.

Progressive Muscle Relaxation (PMR) has been shown to have favorable effects on both the body and mind relative to mental health.



While many factors can certainly impede the health of our gut microbiome, it is empowering to know that so many factors in our control can help support this vast system so interconnected to all aspects of our health, especially our mental health. While we can't control the genes we were born with, we can significantly influence how those genes get expressed to support our mental and physical health. Consuming nutrient-dense, anti-inflammatory, whole foods that support our microbiome and mental health, as well as taking care of ourselves with factors such as getting adequate rest, hydration, and movement, are all important to our mental and microbiome health. This area of research will continue to emerge with more and more valuable insights into improving mental health treatment efficacy from an integrative and functional approach.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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