The Link Between Gut Bacteria and Mental Health

x-ray image of human head with vegetables for a brain.

The human brain is a complex organ composed of billions of neurons continuously firing electrical signals that control what we do, think, and feel. However, many people do not realize that the human body also has a “second brain!” This “second brain,” located in the gut, is often overlooked but equally important in regulating our behaviors, thoughts, and emotions. In fact, research indicates that factors that disrupt gut health affect the brain and may contribute to mental health disorders such as anxiety and depression. The profound discovery of the gut-brain connection lends an all new meaning to the expression “a gut feeling!” Listening to and taking care of our guts may represent a new frontier in the prevention and treatment of mental health disorders!

What is the “second brain?”

Mental illness is unfortunately quite common in the United States. Current statistics indicate that one in six American adults has a mental illness such as depression or anxiety. (1) The conventional medical approach to treating mental health disorders focuses heavily on medication and views the brain as an entity distinct from the rest of the body. However, an emerging body of research indicates that the gut and brain are intrinsically linked and that the health of one organ significantly influences the other.

The “second brain” in the gut is comprised of gut bacteria and a branch of the nervous system called the enteric nervous system. Gut bacteria produce metabolites that modulate the enteric nervous system, which subsequently sends signals to the brain that influence mental function. Depending on the type of bacteria present in the gut, these signals may promote a healthy mental state or may induce conditions such as anxiety, depression, bipolar disorder, and even schizophrenia. (2)

A growing body of scientific studies demonstrates the association between gut bacteria and mental health. In animal studies, mice with lower levels of beneficial Lactobacilli have been found to be less resilient in stressful situations and more prone to depression. (3) In humans, depressed patients have demonstrated significantly altered gut microbiome composition compared to healthy controls, with a preponderance of pathogenic bacteria and lower levels of beneficial bacteria. (4) Patients with bipolar disorder and obsessive-compulsive disorder also have significantly altered gut microbiomes.5,6 This research suggests that the “second brains” of patients with mental health disorders are miscommunicating with the brain, leading to unhealthy alterations in mental function.

Gut bacteria alter neurotransmitter levels and the stress response

Researchers have uncovered two potential mechanisms by which gut bacteria interact with the enteric nervous system, and subsequently, the brain itself:

1. Pathogenic gut bacteria, which predominate when the microbiome is imbalanced, produce metabolites that promote an inflammatory immune response and increase the activity of the sympathetic nervous system. The sympathetic nervous system is the branch of the central nervous system responsible for the “fight or flight” response. (7) Activation of this response produces anxiety. Conversely, beneficial gut bacteria, such as Lactobacilli and Bifidobacteria, produce compounds that suppress inflammation and the sympathetic nervous system reaction.

2. Certain gut bacteria produce neurotransmitters, such as serotonin, that communicate with the brain via the vagus nerve, which connects the enteric nervous system of the gut to the brain. Bacterial imbalances in the gut may alter neurotransmitter levels and disrupt mental health. (8)

Strategies for balancing the microbiome and optimizing mental health

To achieve optimal mental health, it is crucial that we establish a healthy gut microbiome. By eating a nutrient-dense, whole foods diet, supplementing with probiotics, limiting antibiotic use, and reducing stress in our lives, we can create a healthy and happy gut and brain!

Eat a Whole Foods, nutrient-dense diet

Studies show that traditional, whole foods are superior for mental health. (9) One of the reasons why a whole foods diet benefits mental health is because it contains prebiotic fiber, a type of fiber that feeds beneficial gut bacteria and fuels their many metabolic activities, including the production of metabolites that quell inflammation and optimize brain function. Fascinatingly, research has found that supplementation with prebiotic fiber alone lowers cortisol, a hormone involved in the stress response.10 Prebiotic fiber can be found in supplemental forms such as inulin and galactooligosaccharides (GOS), as well as in foods such as asparagus, garlic, onions, leeks, apples, and legumes. Consuming fermented foods such as sauerkraut and kimchi may also benefit mood by supplying the gut with live, probiotic bacteria. When gut bacteria are well-fed and happy, they help create a happy, healthy brain!

Probiotics: Natural antidepressants

Research indicates that probiotics may act as natural antidepressants by producing metabolites that suppress inflammation and the sympathetic nervous system response. In animal models of psychological stress, supplementation with Bifidobacterium infantis, Lactobacillus helveticus, and Lactobacillus rhamnosus has been found to reduce anxiety and depressive behaviors.11,12,13

In human trials, probiotic supplementation also improves parameters of mental health. In one study, supplementation with a multispecies probiotic containing Lactobacilli and Bifidobacteria reduced self-reported sad mood and negative thoughts in adults.14 In another study, supplementation with Bifidobacterium longum reduced subjective levels of stress and improved memory.15 These findings suggest that taking a multispecies probiotic containing Lactobacilli and Bifidobacteria may be a simple and effective way to significantly improve mental health!

Strictly limit antibiotic use

Disruption to the gut microbiome by antibiotics has been found to impair cognition by disturbing the balance of beneficial and pathogenic bacteria in the gut and the neuroactive substances they produce.16 To promote optimal mental health, limit antibiotic use to times when it is essential, and always be sure to take a probiotic to restore beneficial gut bacteria once the course of antibiotics has been completed.

Reduce stress

Psychological stress perpetuates a vicious cycle of poor mental health by lowering levels of beneficial bacteria and increasing levels of bacteria that promote inflammation and the sympathetic nervous system response.17 Stress-reduction practices such as yoga and meditation may benefit mental health by helping you maintain a healthy “second brain.”

Mental illness: It’s not “all in your head!”

If you or someone you love has experienced depression, anxiety, or other mental health issues, know that it is not “all in your head”; in fact, much of the problem may lie in your gut! Our growing understanding of the gut-brain connection represents a new frontier in the treatment of mental health disorders and means that mental health problems need not be a life sentence. By restoring balance to the gut microbiome using a whole foods diet, probiotics, and stress reduction techniques, it is entirely possible to improve your mood and create optimal mental health that lasts a lifetime.

Article by: Lindsay Christensen, BS, biomedical science with an emphasis in nutrition, is a health writer and researcher. She is working on a MS degree in human nutrition toward being a clinical nutritionist. Her passion for natural health and wellness is driven by personal experience of recovering from a serious chronic illness. She offers health coaching and nutrition consulting services and writes about her ancestral, nature-inspired approach to nutrition and healthy living at Ascent to Health:


1. Mental illness. National Institute of Mental Health. Updated November 2017. Accessed January 22, 2018.

2. Deans E. Microbiome and mental health in the modern environment. J Physiol Anthropol. 2016; 36:1. [online]. Accessed January 22, 2018.

3. Marin IA, Goertz JE, Ren T, et al. Microbiota alteration is associated with the development of stress-induced despair behavior. Sci Rep. 2017; 7: 43859. Accessed January 24, 2018.

4. Naseribafrouei A, Hestad K, Avershina E, et al. Correlation between the human fecal microbiota and depression. Neurogastroenterol Motil. 2014; 26(8): 1155-1162. Accessed January 24, 2018.

5. Evans SJ, Bassis CM, Hein R, et al. The gut microbiome composition associates with bipolar disorder and illness severity. J Psychiatr Res. 2017; 87: 23-29. Accessed January 24, 2018.

6. Rees JC. Obsessive–compulsive disorder and gut microbiota dysregulation. Med Hypotheses. 2014; 82(2): 163-166. Accessed January 25, 2018.

7. Bailey MT, Dowd SE, Galley JD, et al. Exposure to a social stressor alters the structure of the intestinal microbiota: implications for stressor-induced immunomodulation. Brain Behav Immun. 2011; 25(3): 397-407. Accessed January 25, 2018.

8. Forsythe P, Bienenstock J, Kunze WA. Vagal pathways for microbiome-brain-gut axis communication. Adv Exp Med Biol. 2014; 817: 115-133. Accessed January 25, 2018.

9. Rahe C, Unrath M, Berger K. Dietary patterns and the risk of depression in adults: a systematic review of observational studies. Eur J Nutr. 53(4): 997-1013. Accessed January 25, 2018.

10. Schmidt K, Cowen PJ, Harmer CJ, et al. Prebiotic intake reduces the waking cortisol response and alters emotional bias in healthy volunteers. Psychopharmacology (Berl). 2015; 232(10): 1793-1801. Accessed January 25, 2018.

11. Desbonnet L, Garrett L, Clarke G, et al. Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. Neuroscience. 2010; 170(4): 1179-1188. Accessed January 25, 2018.

12. Ohland CL, Kish L, Bell H, et al. Effects of Lactobacillus helveticus on murine behavior are dependent on diet and genotype and correlate with alterations in the gut microbiome. Psychoneuroendocrinology. 2013; 38(9): 1738-1747. Accessed January 25, 2018.

13. Bravo JA, Forsythe P, Chew MV, et al. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci USA. 2011; 108(38): 16050-16055. Accessed January 25, 2018.

14. Steenbergen L, Sellaro R, van Hemert S, et al. A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood. Brain Behav Immunol. 2015; 48: 258-264. Accessed January 25, 2018.

15. Allen AP, Hutch W, Borre YE, et al. Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology, and neurocognition in healthy volunteers. Transl Psychiatry. 2016; 6(11): e939.!po=2.17391. Accessed January 25, 2018.

16. Forhlich EE, Farzi A, Mayerhofer R, et al. Cognitive impairment by antibiotic-induced gut dysbiosis: Analysis of gut microbiota-brain communication. Brain Behav Immun. 2016; 56:140-155. Accessed January 25, 2018.

17. Foster JA, Rinaman L, Cryan JF. Stress & the gut-brain axis: Regulation by the microbiome. Neurobiology of Stress. 2017; 7: 124-136.

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