How Your Gut Health Affects Your Mental Health

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Key Information

Gut bacteria affect mental health

The gut microbiome influences brain development, physiology, psychology, and behavior.

Gut dysbiosis can cause diseases

Imbalances in gut bacteria can contribute to multiple sclerosis, irritable bowel syndrome, autism, and depression.

Gut health can be improved by nutrition

Eating fermented foods, probiotics, and prebiotics can help nourish and restore the gut microbiome.

Gut-brain axis research is emerging

Scientists are exploring the mechanisms and potential of gut bacteria in preventing and treating cognitive disorders.

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New research is shedding light on how the gut influences overall health

There is an emerging field of nutritional mental health that looks at holistic factors when treating cognitive disorders.

Mental health is not merely a question of what happens inside your head. It’s difficult to fully separate what occurs in your brain, and what occurs in the rest of your body.

In particular, new research is shedding light on how your gut health may influence cognition.

Your intestines are filled with helpful bacteria that help digest food and regulate metabolism. Some researchers estimate that about 100 trillion bacteria from up to 1000 distinct bacterial species co-inhabit the human GI tract, in different proportions among individuals.1Aziz Q, et al. Gut microbiota and gastrointestinal health: current concepts and future directions Neurogastroenterol Motil. 2013

Keeping this biome of microorganisms happy and healthy could play a huge role in lowering inflammation, oxidative stress, and improving mitochondrial function, all of which can have a drastic impact on systems well outside the GI tract, including cognition.2Bonnie J. Kaplan, et al. The Emerging Field of Nutritional Mental Health: Inflammation, the Microbiome, Oxidative Stress, and Mitochondrial Function, Clinical Psychological Science. 2015

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How Does Gut Bacteria Affect The Brain

Researchers are just now exploring all the different ways that the gut biome can influence mental health.

Advances in sequencing technology have enabled the exploration of the role of the gut microbiota in a broad range of neurological and psychiatric disorders and diseases.

This enables large-scale analysis of self-reported conditions such as the Earth Microbiome Project, which includes sample contributions from over 10,000 citizen-scientists together with an open research network to compare human microbiome specimens.3McDonald D, et al. American Gut: an Open Platform for Citizen Science Microbiome Research mSystems. 2018

What researchers are finding is that gut microbiota plays an active role in processes linked to brain development and physiology, psychology, and behavior.

Neural, endocrine, and immune communication lines tightly link the human gut microbiota with the host central nervous system. In other words, your brain and stomach are inextricably connected.4Cryan JF, Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour Nat Rev Neurosci. 2012

Microbial metabolism can influence the brain through the production of hormones, neurotransmitters, immune system modulators, and short-chain fatty acids like Butyrate.

Tryptophan metabolism in the gut produces important neurotransmitters like serotonin and melatonin, which are critical for mental and emotional regulation.5Gao J, et al. Impact of the Gut Microbiota on Intestinal Immunity Mediated by Tryptophan Metabolism Front Cell Infect Microbiol. 2018

Diseases Affected By Gut Bacteria

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A digestive system that’s out of whack may lead to a variety of health issues

The dysregulation of gut bacteria can at least partially cause multiple diseases.

Multiple sclerosis (MS) is a chronic neuroinflammatory disease of the central nervous system. Several studies show that patients with MS exhibit poor metabolism in their gut biome.

Although the mechanism by which this might influence MS is unknown, it is clear that some connection deserves further study.6Freedman SN, et al. The “Gut Feeling”: Breaking Down the Role of Gut Microbiome in Multiple Sclerosis, Neurotherapeutics. 2018

Emerging data reveal an interaction between psychiatric disorders and Irritable Bowel Syndrome (IBS). This includes generalized anxiety disorder, panic disorder, major depressive disorder, and bipolar disorder.

IBS is partially characterized by disturbed gut flora and inflammation.7Fadgyas-Stanculete M, et al. The relationship between irritable bowel syndrome and psychiatric disorders: from molecular changes to clinical manifestations J Mol Psychiatry. 2014

Gut flora may be one of several environmental factors that contribute to Autism.8Karimi P, et al. Environmental factors influencing the risk of autism, J Res Med Sci. 2017

Gut Microbiome and Depression

Major Depressive Disorder (MDD) is a debilitating psychiatric illness that affects an estimated 300 million people worldwide.

Despite significant advances in our understanding of MDD, existing knowledge is incomplete, treatments are often inadequate, and new insights are urgently needed.

One new area of investigation related to depression is the gut microbiome.

A growing body of literature supports and characterizes a gut-brain axis, and investigates a possible role of gut microbiome dysfunction in major depression.

Inflammation and gut barrier health often show up in studies between the gut microbiome and depression. Depression and anxiety symptoms increase with functional gut disorders.9Maes M, Kubera M, Leunis JC. The gut-brain barrier in major depression: intestinal mucosal dysfunction with an increased translocation of LPS from gram-negative enterobacteria (leaky gut) plays a role in the inflammatory pathophysiology of depression Neuro Endocrinol Lett. 2008 10Pinto-Sanchez MI, et al. Anxiety and Depression Increase in a Stepwise Manner in Parallel With Multiple FGIDs and Symptom Severity and Frequency Am J Gastroenterol. 2015

Animal studies support the idea that a disruption of the microbiome may play a role in depression-like behaviors. Antibiotic administration in mice leads to dysbiosis, depression-like behavior, and altered neuronal hippocampal firing.

However, this can be reversed by repopulating their intestines with probiotics.11Guida F, et al. Antibiotic-induced microbiota perturbation causes gut endocannabinoidome changes, hippocampal neuroglial reorganization and depression in mice Brain Behav Immun. 2018

In cell culture studies, researchers found that gut microbiota makes precursors to neurotransmitters, such as tryptamine.

This can lead to an increase in important transmitters such as serotonin, dopamine, and norepinephrine in the brain, which are primary factors in mood and emotional stability.12Williams BB, et al Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine Cell Host Microbe. 2014 13Barrett E, et al. γ-Aminobutyric acid production by culturable bacteria from the human intestine, J Appl Microbiol. 2012

One animal study found that probiotics containing Lactobacillus plantarum led to both antidepressant-like effects in mice as well as increases in levels of serotonin and dopamine in the brain.

Hopefully, more trials on human subjects will be forthcoming soon.14Liu WH, et al. Alteration of behavior and monoamine levels attributable to Lactobacillus plantarum PS128 in germ-free mice Behav Brain Res. 2016

Can Gut Bacteria Cause Anxiety and Depression?

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Some mental health issues may be actually be connected to the health of your stomach

Abnormalities in this microbiota-gut-brain axis have emerged as a key component in depression, leading to more research attempting to understand the neuroactive potential of the products of gut microbial metabolism.15Caspani G, et al. Gut microbial metabolites in depression: understanding the biochemical mechanisms Microb Cell. 2019

The future of gut-brain axis research involves moving towards the mechanisms underlying the relationship between gut bacteria and depressive behavior.

Gut microbes might affect depressive behavior through mechanisms including direct stimulation of central receptors, peripheral stimulation of neural, endocrine, and immune mediators, and epigenetic regulation of histone acetylation and DNA methylation

In experiments, Brain Derived Nerve Factor (BDNF) expression was reduced in the brains of “germ-free” mice, and this reduction in BDNF correlates to increased anxiety behavior and progressive cognitive dysfunction.16Carlino D, et al. Is altered BDNF biosynthesis a general feature in patients with cognitive dysfunctions?, Neuroscientist. 2013

Gut Bacteria and Alzheimer’s Disease

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Cyanobacteria may play a role in the progression of Alzheimer’s

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the leading cause of cognitive impairment in industrialized societies. The cause of AD is unknown, although the major risk factor for AD is age.17James M. Hill, et al. Pathogenic microbes, the microbiome, and Alzheimer’s disease (AD), Front Aging Neurosci. 2014

There is now evidence that AD may be related to gut biome health.

Most of the changes seen in AD, such as inflammation, brain cell atrophy, immune dysfunction, and cognitive deficits, can also be a consequence of microbial infection.18Heintz C, Mair W. You are what you host: microbiome modulation of the aging process Cell. 2014

There is currently no cure for AD, and it remains unclear how AD originates and propagates throughout the brain and central nervous system.

However, results from recent studies indicate that a significant portion of AD gene signals may be related to environmental and epigenetic factors, including microbes.

The potential contribution of pathogenic microbes to aging and AD is increasingly recognized.19James M. Hill, et al. Pathogenic microbes, the microbiome, and Alzheimer’s disease (AD), Front Aging Neurosci. 2014

Cyanobacteria in the gut can produce BMAA, a neurotoxic amino acid not normally incorporated into protein. This is especially true during periods of stress and inflammation.

BMAA may be a primary contributor to amyloid plaques, which are a hallmark of Alzheimer’s Disease.20Brenner SR. Blue-green algae or cyanobacteria in the intestinal micro-flora may produce neurotoxins such as Beta-N-Methylamino-L-Alanine (BMAA) which may be related to development of amyotrophic lateral sclerosis, Alzheimer’s disease and Parkinson-Dementia-Complex in humans and Equine Motor Neuron Disease in horses, Med Hypotheses. 2013

Lactobacillus in the gut is capable of metabolizing glutamate to produce gamma-amino butyric acid (GABA), the major inhibitory neurotransmitter in the CNS. Dysfunctional GABA-signaling may play a role in cognitive impairment, including AD.21Aziz Q, et al. Gut microbiota and gastrointestinal health: current concepts and future directions Neurogastroenterol Motil. 2013

Gut Bacteria and Neurotoxicity

The microbiome can influence neuroprotection and overall brain health.

Gut bacteria seem to interact with the N-methyl-D-aspartate (NMDA) glutamate receptor, a prominent component in the nervous system that regulates synaptic plasticity and cognition.22Shaheen E. Lakhan, et al. NMDA Receptor Activity in Neuropsychiatric Disorders Front Psychiatry. 2013

For example, the NMDA-targeting and oxidative-stress-inducing neurotoxin BMAA was found elevated in the brains of patients with cognitive damage.

Researchers believe that BMAA is caused by gut microbe dysregulation. So, it stands to reason that lowering BMAA through regulating gut bacteria may actually protect the brain.23Schneider C. The Rush Alzheimer’s Disease Center, Nurs Adm Q. 1990

Gut-Brain Connection and Diet

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Fermented foods may be particularly good for promoting gut health

Ensuring a healthy gut biome (and, therefore, brain) starts with proper nutrition. Eating certain foods can help you maintain the right balance of microbes in your gut.24Robert Hutchins. Microbiology and Technology of Fermented Foods, 2006 These include:

  • Fermented foods (sauerkraut, kimchee, cheese, kefir, yogurt)
  • Vegetables
  • Legumes
  • Starchy roots
  • Fruits
  • Meat and fish.

How To Improve Good Gut Bacteria

Fermented foods contain probiotics, which are beneficial live bacteria that can populate your gut after consumption. It is especially important to consume these foods so that you can form and maintain colonies of helpful bacteria.

Many other foods, especially legumes and vegetables, contain prebiotics, which are starches that help nourish the good bacteria in your stomach and help them flourish.

Consuming a balanced diet full of both probiotics and prebiotics can go a long way towards keeping your stomach bacteria happy.

Do Probiotics Affect Your Mood?

Besides the potential application of probiotics in the treatment of various health conditions like allergies, GI and urogenital tract infections, inflammatory disease, cystic fibrosis, and certain cancers, there is an increasing interest in positive microbiome effects on the central nervous system.25Duncan SH, Flint HJ. Probiotics and prebiotics and health in ageing populations Maturitas. 2013

For example, there is preliminary research on the influence of probiotics and nutritional factors on cognition and mental health.26Camfield DA, et al. Dairy constituents and neurocognitive health in ageing Br J Nutr. 2011

One double-blind, placebo-controlled study saw a significant improvement in mood after six weeks of consuming a probiotic blend. Researchers observed a reduction in depressive mood state, anger, and fatigue, and an improvement in sleep quality.

These findings suggest that probiotics may improve psychological well-being by improving aspects of mood and sleep quality.27Marotta A, et al. Effects of Probiotics on Cognitive Reactivity, Mood, and Sleep Quality, Front Psychiatry. 2019

A meta-analysis of 10 clinical trials found significant improvements in the moods of individuals with mild to moderate depressive symptoms and non-significant effects in healthy individuals.28Ng QX, et al. A meta-analysis of the use of probiotics to alleviate depressive symptoms, J Affect Disord. 2018

However, this metanalysis did note some discrepancies between studies that made comparison difficult. Hopefully, there will be further high-quality studies on this subject in the future.

Which Probiotics Are The Best?

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Several members of the lactobacillus family may be particularly beneficial to the human intestinal biome

What probiotic is best? The short answer is it depends on the person. Each strain should be used for your specific situation.29Francisco Guarner, et al. Probiotics and prebiotics, World Gastroenterology Organisation Global Guidelines. 2017

For example, Lactobacillus plantarum strain 299v has been shown to effectively reduce IBS symptoms, whereas Lactobacillus plantarum strain MF1298 was found to actually worsen IBS symptoms.30Ducrotté P, Sawant P, Jayanthi V. Clinical trial: Lactobacillus plantarum 299v (DSM 9843) improves symptoms of irritable bowel syndrome, World J Gastroenterol. 2012

For general physical and mental health, spore-based probiotics ( a mixture of spores of five Bacillus species) have shown to be the most effective at showing statistically significant improvement in measurements of quality of life.31Catinean A, et al. Bacillus spp. Spores-A Promising Treatment Option for Patients with Irritable Bowel Syndrome, Nutrients. 2019

For mental health, B. longum, B. infanti, L. plantarum, L. helveticus, and L. Rhamnosis all have noted positive effects on mood and anxiety.

So, it is advisable to do your research on which particular strain suits your needs.


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Erik Abramowitz is a certified Nutritional Therapy Practitioner (NTP), Naturopathic Doctoral student, health coach, and father. He is the primary content creator for and the host of the Holistic Nootropics Podcast.

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