The Link Between the Microbiome and Psychological Well-Being

by Amylee Amos MS, RDN

The Gut Microbiome

The human microbiome refers to the ecosystem of microorganisms that live in and on our bodies. These little bugs- bacteria, fungi, parasites, viruses, protozoans- live with us in a symbiotic relationship, meaning that we need them to survive just as much as they need us. In fact, we have 10 times more microbes, most of which are bacteria, in our body than we do human cells (1). So, we’re basically more bug than we are human!

The largest microbiome resides within our gut. This gut microbiome is exceptionally diverse and highly individualistic- our gut microbiome is as unique to each of us as our own fingerprint! The gut microbiome is responsible for countless metabolic reactions. Our gut microbiome has the ability to do all of the following:

  • aid in digestion and absorption of nutrients
  • protect the body against pathogenic (harmful) bacteria
  • assist in detoxification by neutralizing toxins found in foods
  • control the majority of the body’s immune response
  • modulate the body’s inflammatory pathways (2)

The Brain-Gut Connection

Needless to say, we depend on our microbiome for survival. An imbalanced or dysbiotic microbiome has been implicated in many chronic disease states, and the research is still ongoing. The gut, as a result of the microbiome, is intricately connected with the body systems.

Perhaps the most astonishing is the relationship between the gut and the brain. The gastrointestinal tract houses what’s known as the enteric nervous system, which consists of approximately 100 million neurons (3). Yes, you read that correctly- your gut is full of brain cells. While these neurons don’t assist in conscious thought or decision making, they instead allow us to connect with and feel our internal environment. Think about the last time you had to give a big presentation and you felt sick to your stomach? How about the last time you had a ‘gut feeling’ about someone or something. The brain and the gut have the ability to communicate with each other in ways that we are only recently understanding.

Part of this connection is the result of the influence of our gut bacteria on the enteric nervous system. The gut produces an extremely large amount of brain chemicals. It’s estimated that up to 95% of serotonin (the feel good neurotransmitter) in the body is produced in the gut (4). This makes a strong argument for the role of nutrition as a means of microbial rebalance as a treatment for depression, when you consider that the standard treatment of SSRIs for depression function to increase the availability of serotonin. The connection between the brain and gut is so profound that researchers are now calling the gut the ‘second brain.’

The Impact of the Microbiome on Psychological Health

The vagus nerve, which travels from the brainstem to the abdomen, is the primary channel of communication between the gut and the brain. Our gut microbes have the ability to send chemical messages up the vagus nerve to communicate with our brain, just as neurons send information down into the gut, making this communication pathway bidirectional.

Research is now looking into the impact of the composition of the microbiome on psychological health. It turns out that as we lose diversity in the various strains of bacteria in our gut microbiome, we lose functionality- meaning the many functions and responsibilities of the gut microbiota begin breaking down. Beyond the loss of diversity, the presence or absence of certain strains are now being implicated in modulating our position on the continuum from wellness to sickness.

Our psychological health can directly impact the strains of bacteria present in the microbiome. When we are under stress, we create an internal environment that suppresses Lactobacillus and Bifidobacteria, two preferential strains of commensal gut bacteria. Alternatively, feelings of anger and fear increases populations of Bacteriodes fragilis, which is a strain of undesirable pathogenic bacteria (5). Additionally, when we are in a state of chronic stress, our bodies over produce cortisol, which can increase the permeability of our gut lining. This contributes to the condition colloquially known as ‘leaky gut’ (6)

This relationship is bidirectional- not only does psycho emotional state influence our microbiome, but our microbiome has a direct influence on our psycho emotional state. Research done on mice showed that groups with no gut microbes or sterile mice displayed more risk-taking behaviors and stress biomarkers than mice with normal microbiomes (7). Other studies have grouped mice by behavioral attributes and then swapped out their microbiomes. Researchers found that when they gave timid mice the gut bacteria of risk taking mice, their behavior demonstrated more risk taking. The same was true when risky mice were given timid mice microbial transplants- the risk taking behaviors subsided and they became more timid (8). These studies are incredible! Just by changing the composition of the gut microbiome, the mice had a dramatic change in behavior. Smaller studies have also been done in humans, and the results show the same patterns- changes in the gut microbiome result in behavior changes and changes in mood- and these results can and have been measured objectively through tools like functional MRIs (9) .

Keeping Your Microbiome Healthy

What all of this means is that tending to the health of our microbiome is imperative to achieve optimal overall health, including our mental and psychological health. We need to keep our microbiome diverse and heavily populated with commensal bacterial colonies. There are a number of ways to keep our microbiome happy and thriving, but the most influential factor related to the health of the microbiome is the food we eat (10). Stay tuned for future blog posts about eating to maintain a healthy microbiome.


  1. Turnbaugh et al. (2007). The human microbiome project. Nature 449, 804–810.
  2. Perlmutter, D. (2015). Brain Maker. New York, NY: Little, Brown and Company.
  3. Carpenter, S. (2012). That gut feeling. American Psychological Association, 43, 8.
  4. Hadhazy, A. (2010). Think Twice: how the gut’s “second brain” influences mood and well-being. Scientific American. Retrieved from:
  5. Bailey, M.T. & Coe, C.L. (1999). Maternal separation disrupts the integrity of the intestinal microflora in infant rhesus monkeys. Developmental Psychobiology, 35, 2: 146-155.
  6. Vanuytsel et al. (2014). Psychological stress and corticotropin-releasing hormone increase intestinal permeability in humans by a mast cell-dependent mechanism. Gut, 63, 8.
  7. Neufeld et al. (2011). Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterology, 23, 3.
  8. Berick et al. (2011). The intestinal microbiota affect central levels of brain derived neurotrophic factor in behavior mice. Gastroenterology, 141, 2.
  9. Tillisch et al. (2013). Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology, 144, 7.
  10. Sanz, Y. (2010). Effects of a gluten-free diet on gut microbiota and immune function in healthy adult humans. Gut Microbes, 1(3), 135–137.