Skip to main content

Verified by Psychology Today


Treating Mental Health Through the Microbiome

How our microflora affects more than just our gut.

Key points

  • Traditional mental health treatments have focused on the brain.
  • Numerous research studies have demonstrated a link between gut health and health conditions.
  • Cohesive mental health treatment requires understanding how the microbiome may influence mental health and ways to utilize this treatment.
Marharyta Marko/istock
Source: Marharyta Marko/istock

For decades, the treatment of mental health issues such as depression has focused on the brain and brain functioning. Depression has been understood as a disease of the brain, and research focused on associated neurological components (Ross et al., 2015).

Psychopharmacology focuses on the correlation between psychotropic medication and symptom reduction. Certain psychotherapies aim to target maladaptive thinking patterns, schemas and resulting behaviors, and even alternative treatments, such as TMS (transcranial magnetic stimulation) and neurofeedback, focus on regulating brainwave states.

But the brain does not exist in isolation, rather it's a component of a larger systemic function. Symptoms of mental health conditions, such as depression, are not limited to mental and emotional symptomatology, but also present largely as physiological symptoms (e.g., weight gain/loss, insomnia, gastrointestinal distress, lethargy, fatigue, and even hair loss). As such, understanding mental health struggles from a systemic perspective, including the immune system, gut, and microbiome is important in the cohesive treatment of such conditions.

Illness and Gut Health

What do we know about illness in general? According to numerous studies, the diversity of the gut microbiome of ill individuals is significantly lower than healthy individuals. Or, individuals who struggle with certain health conditions may suffer from an overgrowth of a certain type of bacteria. For example, Crohn’s disease has been linked with the over abundance of Bacteroidetes and a decrease of Firmicutes (Wright et al., 2015), lupus has been associated with the relative abundance of certain bacterial species that trigger inflammatory function (Yacoub, et al., 2017), and Ochoa-Reparaz, et al. (2018) demonstrated that alterations in the gut microbes of mice affect the severity of central nervous system inflammatory demyelination that is often seen in multiple sclerosis. Overall, a diverse microbiome has been shown to enhance healthy immune functioning resulting in less systemic illness.

The Microbiome and Mood

Understanding the correlation between the microbiome and mental health first takes an understanding of how the microbiome affects mood. There have been numerous research studies that suggest lack of gut biodiversity can affect neurotransmitter functionality and decrease signals via the vagus nerve.

One interesting study, by Vitetta et al. (2014), found that depression was accompanied by the activation of immune-inflammatory pathways. It was demonstrated that when mice with imbalanced gut flora were given a probiotic with Lactobacili, GABA in the brain was increased, which influenced signaling via the vagus nerve. This stabilized mood and behavior. Further, "anxious rats" that were treated with probiotics showed lower levels of anxiety, fear, and a decrease in stress hormones.

Tillisch et al. (2013), state that probiotics may improve symptoms of depression through anti-inflammatory actions, raising the possibility that this internal inflammatory response slows signaling via the gut-brain axis possibly creating neurotransmitter imbalance along the way.

Treating Mental Health Through the Microbiome

So, what does this mean for the future of mental health treatment? Mental health treatment has historically emphasized medication and therapy. Many of the clients I’ve worked with have been less educated on the gut-brain connection and were traditionally told to comply with medication management and make their therapy appointments. Although most of these individuals did report improvement in their symptoms, I would often hear “I’m better, but I’m just not there yet.” Those clients that took it a step further and worked on lifestyle changes, including nutrition and exercise, experienced even greater symptom relief. But eating ‘healthy’ also isn’t enough. It’s understanding how specific food and lifestyle choices affect our own unique systems.

Which Foods and Supplements Can Help Mental Health?

There is still much debate over which diet is best, and it may continue to be difficult to say due to the unique functioning of each individual’s system. However, the research seems to align with the following:

By far the greatest detriment to our health is processed foods. These foods are loaded with preservatives, nitrates, trans fats, and sugars. In addition to lower nutritional values, these types of foods can cause a major inflammatory response in our system due to these preservatives and other ingredients. Processed foods are associated with decreased microbial diversity in the gut, as well as an increase in "bad" gut bacteria.

Studies have also shown a significant correlation between vitamin D and gut flora. Yamamoto and Jorgensen (2020), cited numerous studies that demonstrated that autoimmune diseases tend to share a predisposition for vitamin D deficiency, subsequently increasing the body's inflammatory response. Further, studies also demonstrated the link between conditions such as depression with a lack of vitamin D. Increasing vitamin D intake may play a role not only in boosting gut flora, but also in curbing symptoms of depression, anxiety, or other mental health concerns.

Finally, there is a strong link between fiber and gut flora. According to Cronin et al., 2021, the emergence of low-fibre “Western diets” associated with industrialized nations is linked to an increased prevalence of gut diseases such as inflammatory bowel disease, obesity, type II diabetes mellitus, and metabolic syndrome. As such, a high-fiber diet can potentially decrease the inflammatory response by modifying the pH and the permeability of the gut. The resultant reduction in inflammatory compounds may alter neurotransmitter concentrations to reduce symptoms of depression (Swann et al., 2020).

Ideally, the interconnection between traditional mental health treatments and gut health is worthwhile. This includes taking medication, going to therapy, but also removing foods or lifestyle choices causing leaky gut symptoms, as well as increasing gut flora. More recently, the term "psychobiotics" has been used to describe the treatment of mental health conditions through pre/probiotics and gut heath. Physical health conditions are often viewed from a systemic lens, and perhaps mental health is no different. Encompassing a biopsychosocial model means including the "bio" piece for the entire system, including the brain. It will be interesting to see trends in mental health treatment as more research is conducted in this area in the near future. Perhaps, the future of mental health really does live in the gut.


Cronin P., Joyce, S.A., O’Toole, P.W., and O’Connor, E.M. (2021). Dietary Fibre Modulates the Gut Microbiota. Nutrients: 13 (5): 1655:

Ocho-Reparaz, J., Kirby, T.O., Kasper, L.H. (2018). The gut microbiome and multiple sclerosis. Cold Spring Harbor Perspectives in Medicine 8 (6):

Ross, D.A., Travis, M.J. and Arbuckle, M.R. (2015). The future of psychiatry as clinical neuroscience: Why not now? JAMA Psychiatry 72, 413-414.

Swann, O.G., Kilpatrick, M., Breslin, M., and Oddy, W.H. (2020). Dietary fiber and its associations with depression and inflammation. Nutr Rev: 78 (5): 394-422. doi: 10.1093/nutrit/nuz072.

Tillisch, K., Labus, J., Kilpatrick L. et al (2013). Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology 144:1394-1401

Vitett, L., Bambling, M., Alford, H. (2014). The gastrointestinal tract microbiome, probiotics, and mood. Inflammopharmacology DOI 10.1007/s10787-014-0216-x

Wright, E,K., Kamm, M.A. Teo, S.M., Inouye, M., Wagner, J., and Kirkwood, C.D. (2015). Recent advances in characterizing the gastrointestinal microbiome in crohn’s disease: A systemic review. Inflammatory Bowel Diseases 21(6): 1219-1228.

Yacoub, R., Jacob, A., Wlaschin, J., McGregor, M., Quigg, R.J., and Alexander, J.J. (2018). Lupus: The microbiome angle. Immunobiology 223(6-7) 460-465.

More from Claudia Skowron MS, LCPC, CADC
More from Psychology Today