Who’s Really In Control? How Your Gut Microbiome Impacts Your Mental Health

Article Revised 02.27.2026

Our incredible minds are what differentiate us from other creatures.

We have the unique ability to reason, think abstract thoughts, and experience deep emotions. Yet, emerging research is finding that our gut microbes are the invisible hand influencing our mental well-being.

That’s right – there is a two way street of communication along what’s called the gut-brain axis occurring at all times between the enteric system in your gut and the central nervous system – and your microbes play a dominant role. Increasing evidence has found the gut microbiome plays a more dominant role in this conversation than we originally thought. [1]

Your gut microbiome even helps create neurotransmitters and metabolites that act on your brain via the vagus nerve. This has led to a wave of new studies investigating how the gut microbiome influences our brain and how we can leverage this to improve our mental health.

Neuroscientist John Cryan from University College Cork in Ireland has been studying the power of the gut microbiome in fascinating experiments using mice models. By altering, eliminating, or preventing the development of a healthy microbiome in the  the mouse, Cryan found:

• Mice without gut microbes (germ-free) experience neurochemical changes within the brain [2]
• Germ-free mice are unable to recognize other mice around them, making them unable to socialize [3]
• Germ-free mice exhibit high-risk behavior [2]
• Mice without microbes are unable to remember scary situations, suggesting the microbiome impacts neurological pathways involved in fear conditioning [4]

Another team of researchers from McMaster University in Ontario, Canada found that when microbes were taken from a ‘normal’ mouse and transplanted to the gut of a germ-free mouse through a procedure known as fecal microbiota transplantation, it altered the brain chemistry and behavior of the formerly germ-free mouse. Essentially, the mouse adopts a similar personality to its donor. [5]

Pretty incredible, isn’t it?

It makes you wonder, who’s really in control here?

The gut microbiome is clearly influential in certain actions and behaviors that were fully credited to the brain, suggesting it’s time we stop thinking that our brain is in full control.

Research Suggests Food is Medicine

Based on his studies, Cryan concludes, “ dietary treatments could be used as either adjunct or sole therapy for mood disorders.” [6]

This touches on one of the most exciting insights that has come from gut microbiome research, which is that we have the power to change the composition of our gut microbiota through our diet. Each microbe prefers certain food – just like you and me, making every meal you eat important because you are feeding your microbes.

Until recently we’ve been treating mental health with medications to target chemical imbalances of the brain, but it appears we may have been looking at the wrong brain.

When you imagine your body, imagine you have two brains – your classic brain and your gut.

Understanding Your Second Brain

Due to how powerful your gut is in influencing your mental state, it’s earned itself the nickname – the second brain. Your enteric nervous system (ENS) is embedded in the walls of your gut and contains between 200-600 neurons, which is more than your spinal cord. Your ENS is incredibly impressive and works both independently and together with central nervous system (CNS). [7]

The gut microbiome directly influences the development, function, and activity of the ENS. [8] One of the ways the gut microbiota is able to communicate with the nervous systems is through intrinsic primary afferent neurons (IPANs). IPANs are specific neurons that reach into the gut lining and respond to changes in the gut lumen. IPANs are transducers, meaning they can take physiological stimuli and change them into electrical signals. [9]

Examples of physiological stimuli IPANs respond to include:

• Changes in gut chemistry (including gut microbial activity)
• Movement of the villi (finger-like folds in the gut lining)
• Distortion of gut lining (normal for digestion)
• Contractions of intestinal muscle (also, normal for digestion)

Through IPANs and the neurotransmitters created by the gut microbiome, what happens in our gut can be communicated to the brain.

Due to this intricate connection between our two brains, the study of the gut microbiome is arguably the fastest growing area of mental health research.

The Gut Microbiome and Mental Health

As researchers continue to explore how the gut and brain communicate, growing scientific interest is focused on how the gut microbiome may relate to brain function, behavior, and overall mental well-being.

Gut microbiome and attention-related traits

Early research suggests that variations in gut microbial populations may be observed in individuals who experience attention and impulse-related challenges. Some studies are exploring how these microbial differences may relate to neurotransmitter activity and reward signaling pathways that influence focus and behavior. These findings are preliminary and continue to be actively investigated. [12]

Gut microbiome, stress, and compulsive tendencies

Stress, dietary changes, and antibiotic use are known to influence gut microbial balance. Researchers are examining whether these shifts may be associated with changes in behavior patterns and stress responsiveness in certain individuals. Interest remains high in understanding how maintaining a balanced microbiome may support resilience to stress. [13]

Gut microbiome and mood-related pathways

Research examining gut microbial patterns in individuals experiencing significant mood variability is still in early stages. Initial studies suggest that the gut microbiome may interact with inflammatory, metabolic, and neurotransmitter pathways involved in brain function, though much remains to be understood. [14]

Overall, scientific exploration of the gut–brain axis continues to expand. Emerging areas of research—including dietary strategies and microbiome-focused interventions—are being studied for their potential role in supporting gut health, which is increasingly recognized as an important component of overall wellness and mental resilience. [15]

Your Microbes Are Your Buds

It’s time to start thinking of microbes as our buds. This means we have to be mindful of unnecessary antibiotic use, harsh cleaning chemicals, sanitizers, and anything else that hurts their chances of survival.

Most of your gut microbes live in a mutualistic relationship with you. They selfishly want you to stay healthy so that they can thrive. Your microbes participate in many biological functions including maintaining your body’s homeostasis – primarily by supporting your immune system. For these little guys to do their jobs and live happy, healthy lives, they need just the right environment, which you control through your diet.

The gut microbiome is an active habitat of microbes and just like any other environment, it is  healthiest when it’s balanced. We often refer to the environment of the gut microbiome as the milieu. As part of the human species, our gut microbiomes have core similarities, though we each have a unique microbial profile – think of this as your microbial fingerprint.

Because each person’s gut microbiome is particular to them, there is no universal diet that’s good for everyone. This is where Viome comes in.

Viome’s powerful metatranscriptomic technology and advanced AI analysis AI analysis helps you identify the diet for you and your gut microbiome. Your Viome food recommendations tell you exactly what to eat to feed beneficial microbes, and maintain a balanced microbiome.

Resources:

1. Carabotti M, Scirocco A, Maselli MA, Severi C. (2015). Ann Gastroenterol. 2015 Apr-Jun;28(2):203-209. PMID: 25830558; PMCID: PMC4367209.
2. Neufeld KM, Kang N, Bienenstock J, Foster JA. (2011). Neurogastroenterol Motil. 2011 Mar;23(3):255-64, e119. doi: 10.1111/j.1365-2982.2010.01620.x. Epub 2010 Nov 5. PMID: 21054680.
3. Luczynski P, McVey Neufeld KA, Oriach CS, Clarke G, Dinan TG, Cryan JF. (2016). Int J Neuropsychopharmacol. 2016 Aug 12;19(8):pyw020. doi: 10.1093/ijnp/pyw020. PMID: 26912607; PMCID: PMC5006193.
4. Hoban AE, Stilling RM, Moloney G, Shanahan F, Dinan TG, Clarke G, Cryan JF. (2018). Mol Psychiatry. 2018 May;23(5):1134-1144. doi: 10.1038/mp.2017.100. Epub 2017 May 16. PMID: 28507320; PMCID: PMC5984090.
5. Collins SM, Kassam Z, Bercik P. T. (2013). Curr Opin Microbiol. 2013 Jun;16(3):240-5. doi: 10.1016/j.mib.2013.06.004. Epub 2013 Jul 8. PMID: 23845749.
6. Schmit, C. (2015, Mar 1). Blog, Scientific American. Online at scientificamerican.com
7. Furness JB, Callaghan BP, Rivera LR, Cho HJ. (2014). Adv Exp Med Biol. 2014;817:39-71. doi: 10.1007/978-1-4939-0897-4_3. PMID: 24997029.
8. Hyland NP, Cryan JF. (2016). Dev Biol. 2016 Sep 15;417(2):182-7. doi: 10.1016/j.ydbio.2016.06.027. Epub 2016 Jun 22. PMID: 27343895.
9. Furness JB, Jones C, Nurgali K, Clerc N. (2004). Prog Neurobiol. 2004 Feb;72(2):143-64. doi: 10.1016/j.pneurobio.2003.12.004. PMID: 15063530.
10. Clapp M, Aurora N, Herrera L, Bhatia M, Wilen E, Wakefield S. (2017). Clin Pract. 2017 Sep 15;7(4):987. doi: 10.4081/cp.2017.987. PMID: 29071061; PMCID: PMC5641835.
11. Zhou L, Foster JA. (2015). Neuropsychiatr Dis Treat. 2015 Mar 16;11:715-23. doi: 10.2147/NDT.S61997. PMID: 25834446; PMCID: PMC4370913.
12. Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT, Arias Vasquez A. (2017). PLoS One. 2017 Sep 1;12(9):e0183509. doi: 10.1371/journal.pone.0183509. PMID: 28863139; PMCID: PMC5581161.
13. Rees JC. (2017). Med Hypotheses. 2014 Feb;82(2):163-6. doi: 10.1016/j.mehy.2013.11.026. Epub 2013 Dec 1. PMID: 24332563.
14. Dickerson F, Severance E, Yolken R. (2017). Brain Behav Immun. 2017 May;62:46-52. doi: 10.1016/j.bbi.2016.12.010. Epub 2016 Dec 18. PMID: 28003152; PMCID: PMC5503102.
15. Kali A. (2016). Biomed J. 2016 Jun;39(3):223-4. doi: 10.1016/j.bj.2015.11.004. Epub 2016 Aug 9. PMID: 27621125; PMCID: PMC6140288.