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Gut Microbiome and Cognitive Function

-Dr. Mary Mollway, Ed.D November 22, 2023

In the last two blogs, we explored what the gut microbiome is and how it forms in infants. In our final installment of this series, we are going to look at how the composition of the microbiome affects brain development, cognition, and cognitive decline.

We have 300-500 different strains of bacteria living in our intestinal tract, known as the microbiome. These bacteria are called microbiota They can communicate with our central nervous system (our brain) and cause changes through the production and secretion of neurotransmitters and by secreting amino acids, short-chain fatty acids, folate, etc.

The microbiota are very sensitive to changes in the environment. Some of the factors that impact it are stress, sleep, diet, environmental chemicals, and medications. When the microbiota gets out of balance, this is known as "dysbiosis". Dysbiosis is leaked to increased gut permeability, or "leaky gut", increasing inflammation. Leaky gut has been associated with inflammatory bowel disease, celiac, allergies, eczema and psoriasis, anxiety, depression, and cognitive issues.

Image: (Dash, Syed, & Khan, 2022)

From the image above. you can see how pivotal the gut microbiota are in the development of the brain and nervous system. Studies have shown a direct correlation between the composition of the microbiota and the size of the hippocampus where we store memories, cognitive flexibility, and executive function. In addition, tests of auditory and verbal learning, rapid automized naming (critical for reading), and processing speed were impacted by the microbiota.

The number one reason children struggle to learn to read is challenges in auditory processing, specifically phonological processing. Godur et al (2023) discuss the relationship between gut dysbiosis and auditory disorders and the use of probiotics and prebiotics to improve auditory function in a variety of disorders.

Bacteria are not the only microbes that impact the gut. The presence of parasites has been found to impact executive function (Mayneris-Perxachs et al, 2022). In this study, working memory, attention, sustained attention, and divided attention were found to be affected by the presence of a specific common parasite.

In other studies, behaviors commonly found in ASD were produced in mice by changing their microbiota, including stimming, social withdrawl, spinning,etc. TACA has a great article about dysbiosis in autism that you can read here.

Common microbes found with dsybiosis include:

  • Colonized bacteria, such as strep b

  • Candida (yeast)

  • C Difficile

  • Clostrydia

  • Staph or MRSA

  • e coli

  • Fungi such as aspergillis

To find out what microbes are impacting the gut balance, a comprehensive stool analysis is the most effective test. Mosaic Diagnostics makes one of the best (formerly Great Plains Laboratories) . Treatment involves eradicating the unwanted microbes and increasing the levels of good microbes. This is generally referred to as a "kill and rebuild" protocol. A qualified naturopath, integrative physician or functional neurologist can order this test for you.

In my private practice, I refer nearly every child for microbiome testing. Every child that I have referred for testing has had significant dysbiosis that included a combination of the microbes listed above. Balancing the microbiome has led to better speech, awareness, cognition, sensory processing, and attention for my clients. If you haven't considered this as an option for your child (or yourself!), it might be time to give this some thought as part of a comprehensive treatment protocol.


Dash, S., Syed, Y. A., & Khan, M. R. (2022). Understanding the Role of the Gut Microbiome in Brain Development and Its Association With Neurodevelopmental Psychiatric Disorders. Frontiers in cell and developmental biology, 10, 880544.

Godur, D. A., Denton, A. J., Eshraghi, N., Mittal, J., Cooper, J., Moosa, M., & Mittal, R. (2023). Modulation of Gut Microbiome as a Therapeutic Modality for Auditory Disorders. Audiology research, 13(5), 741–752.

Liang, X., Fu, Y., Cao, Wt. et al. Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis. Transl Neurodegener11, 49 (2022).

Meyer K, Lulla A, Debroy K, et al. Association of the Gut Microbiota With Cognitive Function in Midlife. JAMA Netw Open. 2022;5(2):e2143941. doi:10.1001/jamanetworkopen.2021.43941

Mayneris-Perxachs, J., Arnoriaga-Rodríguez, M., Garre-Olmo, J. et al. Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function. ISME J16, 2181–2197 (2022).

Tooley K. L. (2020). Effects of the Human Gut Microbiota on Cognitive Performance, Brain Structure and Function: A Narrative Review. Nutrients, 12(10), 3009.

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