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Stress and the Microbiome: A Notable Relationship

Gut reactions and brain health

by Malay Nanavaty

How does stress affect the microbiome?

Most people understand the gut brain axis from personal experience. For example anyone who is about to do something anxiety inducing (public speaking, etc.) will feel a difference in their bowel movements. In the case we just discussed, diarrhea is most common. Similarly, thinking about food can often trigger your gut, inducing hunger pangs and grumbling. With our lifestyles growing more stressful in the modern era, it is possible that your microbiome may be a useful tool to understand in the battle for your sanity.

Signalling in the Gut

All of the examples mentioned above are examples of how the brain and gut affect one another. While those examples are rather obvious, there are many more ways that these two organs communicate. In fact, your very state of mind can be altered by the intercommunication of these two systems. The most common ways these organs communicate is through:
1. Hormonal secretion: Your gut bacteria produce a large amount of hormonal products that may be used in different areas of your body, brain included. The hormone serotonin is largely produced by gut bacteria for example.
2. Intestinal permeability to metabolites: Molecules produced by bacteria in our gut have the ability to get absorbed into our bloodstream and provide our brains with vital information regarding the gut environment.
3. Immuno-endocrine interactions: Bacteria-secreted molecules also are in constant communication with the immune system, ensuring that pathogens are eliminated and beneficial bacteria are safe. These signals to the immune system are also essential in regulating the sensitivity of the body to stressful stimuli. This is because the microbiome has a vested interest in making sure that the immune system is not hyper-responding to perceived threats.

When it comes to stress signalling, there is evidence suggesting that the microbiome has both acute and chronic responses. Studies show that even short term stress can alter the relative populations of different phyla within your gut. These changes promote the growth of bacteria that increase your sensitivity to stress by stimulating your HPA axis (hypothalamic-pituitary-adrenal axis).

The Immune System

Some of the molecules produced by bacteria in a stressed gut modulate the immune system. Since stress is often a time where acute threats take priority over long term safety, it is likely that these changes play a suppressive role and inhibit immune function. On top of that, stress increases gut permeability, enabling bacteria to pierce the mucosal gut layer, triggering inflammation.

Neurodevelopment: Pros and Cons

While these stress-dominant bacteria sound like they are all bad, this is not necessarily true. In fact, some of the bacteria that are hyperactive during stress have critical normal functions such as production of BDNF (brain-derived neurotrophic factor), a hormone essential for maintaining neuroplasticity and development.

Mice Studies on Anxiety Behavior

Lab studies with sterilized mice have shown that both anxiety pathways and normal neurodevelopment are impaired when the microbiome is eliminated. These mice also show altered gene expression in their prefrontal cortexes, specifically in the genes associated with myelin production and cellular metabolism. If the microbiota is depleted during infancy, these mice struggle with a lifelong reduction in hippocampus function. However, adult mice that have already developed neural structures are able to recover from microbiome depletion via exercise and colonization with exogenous bacteria.

Emerging Human Evidence

This evidence is backed by human studies as well, which show a correlation between neurodevelopmental disorders and poor colonization of the microbiome early in life. People who suffer from gut deficiencies such as IBS are often diagnosed with neural issues such as depression and anxiety as well, further attesting to the utility of the microbiome in early neural development.

While it is difficult to alter the long-term microbiome population you host, there is evidence that certain supplements are able to regulate the metabolic pathways your microbiome is expressing. The omega-3 fatty acids have been shown to play a key role in regulating the populations of stress signalling bacteria, possibly due to their ability to reduce inflammation in the gut.


There is a lot of evidence interconnecting stress, the microbiome, and cognitive function. It appears that exposure to intense stressors early in life can leave a lasting impact on the composition of your microbiome which, in turn, promotes hypersensitivity to negative emotions like anxiety for life. These changes in the microbiome may be driven by the changes in gut behavior (contraction, mucus secretion, etc.) as a result of conscious experience. Additionally, stress in adults also has the potential to temporarily alter your microbiome. While the exact nature of these changes is not yet known, it is likely that the microbiome plays an important role in regulating both your cognitive behavior and your immune function in high-stress situations. It is possible that your very thoughts may be influenced by what is going on in your gut community.

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