Exploring the Gut-Microbiome-Brain Axis: Insights into the Role of Microbial Species and Metabolism in Early Cognitive Development


The intricate relationship between the gut and the brain, often referred to as the “gut-brain axis,” is an area of growing scientific interest. This connection is facilitated through multiple pathways, including the autonomic nervous system, the endocrine system, and the vagus nerve. The gut communicates with the brain through various signaling molecules, including endocrine and immune (cytokine) signals.

Notably, the products of microbial metabolism in the gut can also impact the brain, both indirectly by stimulating the enteric nervous and immune systems, and directly through molecules that enter circulation and cross the blood-brain barrier.

Recent research has established causal links between the gut microbiome and neural development, particularly in cases of atypical development. Both human epidemiological studies and animal models have highlighted the influence of gut microbes on the development of conditions like autism spectrum disorder, depression, and Alzheimer’s disease. Despite these advances, there remains a significant gap in understanding how the microbiome-gut-brain axis functions in normal neurocognitive development, especially in the early stages of life.

The first years of life represent critical periods for both the microbiome and the brain. It is believed that fetal development occurs in a sterile environment. However, at birth, newborns are rapidly exposed to microbes through various sources, including the birth canal (in vaginal births), caregivers, breast milk or formula, and other environmental factors.

The early microbiome is characterized by low microbial diversity and is dominated by certain bacterial genera. As infants transition to solid foods, the gut microbiome undergoes a significant transformation, increasing in diversity and resembling more closely the microbiomes found in adults.

This transition is particularly intriguing as it coincides with crucial windows in neural development. During these periods, significant neurodevelopmental processes such as myelination, neurogenesis, and synaptic pruning take place. Understanding the changes in the gut microbiome during this transition is therefore crucial.

In the early years, a child’s brain undergoes dramatic changes in anatomy, microstructure, organization, and function. By age 5, the brain has reached over 85% of its adult size and has established a pattern of axonal connections. These developments occur in sensitive periods (SPs) when neural plasticity is at its peak. Emerging evidence suggests that the gut microbiome may influence the timing and duration of these SPs, highlighting the importance of understanding the normal development of the microbiome and its relationship with neurocognitive development.

To explore this relationship further, a study was conducted on a large cohort of healthy children from infancy through age 10. This study utilized shotgun metagenomic sequencing to assess gut microbial communities, focusing on both taxonomic and gene-functional levels.

Cognitive abilities in these children were measured using various age-appropriate psychometric assessments, and brain structure was assessed using magnetic resonance imaging (MRI). The study employed classical statistical analysis and machine learning (ML) techniques and found a significant link between the development of the gut microbiome, children’s cognitive abilities, and brain structure. It was observed that both microbial taxa and gene functions could predict cognitive performance and brain structure, underscoring the deep interconnection between the gut and the brain.

This research not only enhances our understanding of the microbiome-gut-brain axis but also opens new avenues for early identification and intervention in cases of atypical neurocognitive development. It underscores the potential of gut microbiome studies in providing insights into the complex mechanisms underlying brain development and functioning.


In this discussion chapter, we delve into the intricate relationship between the gut microbiome and brain function, as revealed through our study investigating the gut-microbiome-brain axis in young, healthy children. This research contributes significantly to the field, as it is one of the first to directly investigate the relationship between microbial species, their genes, and typical cognitive development in this demographic.

Understanding the Gut-Brain-Microbiome Axis in Early Life

The early life stages are pivotal, as interventions during this period can have more pronounced and long-lasting effects than those in later life due to the dynamic nature of the gut microbiome and the brain. This underscores the importance of understanding the gut-brain-microbiome axis from an early age. Even if microbial metabolism does not have a direct causal impact, identifying risk factors could guide early intervention strategies, thereby providing significant value.

Microbial Species and Cognitive Function

Our study identified several species within the Eggerthelaceae family, such as A. celatus and Eggerthella lenta, that are associated with cognitive function. These species are known for their unique metabolic activities. For instance, A. equolofaciens’s production of the nonsteroidal estrogen equol and its relation to cognitive functions in specific brain regions such as the right anterior cingulate is particularly intriguing. Furthermore, the study also highlights the potential neuroprotective effects of metabolites produced by other species like Gordonibacter pamelaeae.

Early Microbial Influences on Brain Development

We observed no significant associations between individual microbial species and cognitive performance in our youngest subset (ages 0 to 6 months). This may be attributed to brain developmental trajectories beginning in utero, with microbial influences only manifesting after birth. However, early-life microbiomes were shown to be predictive of future cognitive functions, indicating the long-term influence of gut microbiota on cognitive development.

Microbial Taxa and Brain Structure

The study also revealed associations between certain bacterial taxa and brain structure, aligning with previous findings. For example, Bacteroides species were linked with the size of the left nucleus accumbens and were found to produce neuroactive compounds. This discovery is particularly relevant as it relates to conditions such as attention deficit hyperactivity disorder (ADHD) and substance use disorder.

Cognitive Subscales and Gut-Microbial Connections

Our study further explored the relationship between cognitive subscales and gut microbiota. For instance, we found connections between the thalamus and the expressive language component, and between the central opercular cortex and gross motor development. These findings align with prior research and offer insights into the potential gut-microbial connections influencing cognition and neuroanatomy.

Importance of Species-Level Resolution and Functional Insights

The use of shotgun metagenomic sequencing in our study was crucial as it provided species-level resolution, enabling us to identify specific microbial influences on the brain. This approach surpasses the capabilities of 16S rRNA gene amplicon sequencing, which is limited in its resolution. Additionally, gene-functional insights offered by shotgun metagenomics, particularly regarding the metabolism of short-chain fatty acids (SCFAs) and neuroactive molecules like glutamate, are invaluable for understanding the relationship between microbial metabolism and cognitive development.

Challenges and Future Directions

While our study has provided significant insights, it is not without limitations. For instance, the reliability of cognitive assessments, particularly in younger children, and the influence of external factors such as the COVID-19 pandemic, may introduce variability into the results. Future studies should consider these factors and aim to cover a broader demographic, including traditionally understudied populations, to gain a more comprehensive understanding of the variability in gut microbiomes and their impact on neurocognition.


Our findings establish a clear and statistically significant association between microbial taxa, their functional potential, cognition, and brain structure. While direct causal relationships were not tested, these associations present promising targets for future research, including preclinical models and investigations into microbial metabolism at the molecular level. The potential discovery of neuroactive metabolites could lead to biomarkers for early detection or therapeutically useful compounds, advancing our understanding and management of neurocognitive development and health.

reference link : https://www.science.org/doi/10.1126/sciadv.adi0497


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