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The gut microbiome in neurological disorders

March 18, 2025

  • Brain Health
    Brain Health

    Brain health encompasses the overall functioning and well-being of the brain, including cognitive function, emotional and psychological well-being, neurological integrity, behavioral health, neurodevelopmental health, age-related brain health, and brain resilience and plasticity.

Last Updated: 2024

Microbiome Signatures identifies and validates condition-specific microbiome shifts and interventions to accelerate clinical translation. Our multidisciplinary team supports clinicians, researchers, and innovators in turning microbiome science into actionable medicine.

Karen Pendergrass

Karen Pendergrass is a microbiome researcher specializing in microbiome-targeted interventions (MBTIs). She systematically analyzes scientific literature to identify microbial patterns, develop hypotheses, and validate interventions. As the founder of the Microbiome Signatures Database, she bridges microbiome research with clinical practice. In 2012, based on her own investigative research, she became the first documented case of FMT for Celiac Disease—four years before the first published case study.

What was reviewed?

This review comprehensively examined the emerging role of the gut microbiome in neurological disorders, focusing on the microbiota-gut-brain axis—a bidirectional communication network that links the gut microbiome to central nervous system (CNS) functions. The authors reviewed existing literature and studies that explore how gut microbiota influence neurodevelopment, aging, and the pathophysiology of various neurological disorders, including Alzheimer’s disease, autism spectrum disorder (ASD), multiple sclerosis, Parkinson’s disease, stroke, and traumatic brain injury. The review also examines the potential for microbiome-targeted interventions (MBTIs) as therapeutic strategies in these conditions.

Who was reviewed?

The review primarily focused on:

Animal Models: A significant portion of the evidence comes from studies involving germ-free mice and other animal models, which have been used to demonstrate the impact of the gut microbiota on neurodevelopment, neuroinflammation, and behavior.

Human Studies: The review also included cross-sectional, observational, and interventional studies in human subjects, particularly in populations affected by neurological disorders. These human studies often explored correlations between microbiota composition and disease states, cognitive functions, and responses to microbiome-targeted interventions such as probiotics and dietary changes.

What were the most important findings of this review?

The most important findings of the review include:

Microbiota-Gut-Brain Axis: The gut microbiome plays a crucial role in brain health through multiple pathways, including immune modulation, neurotransmitter production, and regulation of neuroinflammation.

Neurodevelopment: Early-life microbiota composition significantly influences neurodevelopmental processes, with evidence from both animal and human studies suggesting that disruptions in the microbiota-gut-brain axis can affect cognitive and social behaviors.

Aging and Neurological Disorders: A diverse gut microbiome is associated with healthier aging and may protect against cognitive decline. In neurological disorders such as MS, PD, AD, and ASD, altered gut microbiota compositions have been observed, with certain bacterial taxa linked to disease pathophysiology.

Therapeutic Potential: There is growing evidence that microbiome-targeted interventions (e.g., probiotics, prebiotics, dietary changes) may modulate disease outcomes, though the field is nascent, and robust clinical trials are needed to confirm these therapeutic effects.

What are the greatest implications of this review?

The greatest implications of this review are:

Potential for New Therapeutics: Understanding the microbiota–gut–brain axis could lead to novel therapeutic strategies targeting the gut microbiome to treat or prevent neurological disorders. This could involve probiotics, prebiotics, dietary interventions, or fecal microbiota transplantation.

Need for Longitudinal Studies: Many of the findings are based on cross-sectional studies, which provide a snapshot in time but do not establish causality. There is a need for longitudinal cohort studies and randomized controlled trials to better understand how microbiota changes over time in relation to disease progression and treatment response.

Precision Medicine: Integrating microbiome data with other omics (genomics, metabolomics) could help tailor treatments to individual patients based on their microbiota composition, potentially enhancing the effectiveness of therapies for neurological disorders.

Holistic Understanding of Neurological Diseases: The review highlights the importance of considering the gut microbiome as an integral part of understanding and managing neurological diseases, potentially shifting paradigms in neurology towards a more comprehensive systems biology approach.

Integration of Systems Biology: The authors underscore the importance of integrating microbiome research with genomic, metabolomic, and other multiomic data to understand the mechanisms underlying the microbiota-gut-brain axis fully. This approach could lead to the identification of biomarkers and the development of more precise interventions.

Potential for Preventive Measures: The review suggests that modulating the microbiome early in life or during the aging process could serve as a preventive strategy against cognitive decline and other neurological disorders. This could shift the focus from treating diseases after they manifest to preventing them through microbiome management.

Conclusion from the Authors

Recent advances have highlighted the critical role that the gut microbiota plays in both the development and maintenance of brain function. Evidence from a growing body of clinical and animal research strongly supports the involvement of the microbiota in neurological disorders such as Parkinson’s disease, multiple sclerosis, and autism spectrum disorder, with emerging insights into its role in Alzheimer’s disease and stroke. However, the field remains in its early stages, and researchers must exercise caution in interpreting these findings. Small sample sizes, methodological inconsistencies, and potential biases often limit the current body of work. To move forward, there is a pressing need for well-designed, large-scale studies that can accurately elucidate the complex relationships within the microbiota-gut-brain axis.

Future research must shift from observational studies to those that can establish causality and explore functional outcomes. This necessitates a greater emphasis on interventional approaches, such as the use of probiotics, prebiotics, and fecal microbiota transplantation, in longitudinal studies. Such approaches should aim to identify the microbiota as a biomarker of disease and test the efficacy of microbiota-targeted therapies in clinical populations.

Given the considerable interindividual variability in microbiota composition, a significant challenge lies in defining what constitutes a “healthy” microbiome. This variability complicates efforts to develop standardized therapeutic approaches. Nevertheless, it also opens the door to personalized medicine, where treatments are tailored to the individual’s unique microbiome profile. To advance this goal, researchers must delve deeper into the microbial ecosystem, beyond just bacterial genera, employing metagenomic and multi-omic techniques to understand the full spectrum of microbial influence on brain health.

Additionally, expanding research to include other components of the microbiome, such as viruses and bacteriophages, will be crucial to gaining a comprehensive understanding of their role in brain function. Investigating the interaction between host genetics and the microbiome is another underexplored area that holds promise for uncovering the biological mechanisms underlying neurological disorders. Systems biology approaches will be vital for integrating these diverse data streams and providing a holistic view of microbiota-gut-brain interactions.

Diet remains a major factor influencing microbiota composition, especially in the context of neurological disorders that affect nutritional intake. Understanding the relationship between diet, microbiota, and brain health will be key to developing dietary interventions that support neurological health throughout life. As research progresses, the influence of dietary components and microbial metabolites on health will likely become a central focus in the quest to develop microbiota-based therapies.

The interaction between medications and the microbiota is an emerging area of interest, as recent studies indicate that a substantial number of drugs can alter the gut microbiome. This interaction has significant implications for drug efficacy and safety, underscoring the need for further investigation. As we continue to explore these complex relationships, the next five years of research will be pivotal in determining how the microbiota can be harnessed to develop effective therapies for neurological disorders.

Image modified from the original “The gut microbiome in neurological disorders”
Figure 2: Pathways of communication between the microbiota and the brain

Autism spectrum disorder (ASD)

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by social, communication, and behavioral challenges. It involves genetic and environmental factors, including microbiome imbalances which influence symptom severity and overall health.

Microbiome-Targeted Interventions (MBTIs)

Microbiome Targeted Interventions (MBTIs) are cutting-edge treatments that utilize information from Microbiome Signatures to modulate the microbiome, revolutionizing medicine with unparalleled precision and impact.

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