Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders

Oct 28, 2025Acta microbiologica et immunologica Hungarica

Using Artificial Intelligence on Gut Bacteria to Help Predict Brain Diseases That Cause Memory and Movement Problems

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Abstract

AI-driven multi-omics strategies may transform microbiome-based precision medicine in neurodegenerative disorders.

The human gut microbiota is essential for immune function, metabolism, and brain health.
Gut dysbiosis may contribute to neurodegenerative disorders, including Alzheimer's and Parkinson's disease, via the gut-brain axis.
High-throughput sequencing and multi-omics technologies have produced extensive datasets, but clinical application is limited by data variability and complex analysis.
There is a need for reproducible workflows and integrative computational strategies to enhance research consistency.
AI and machine learning can improve understanding of host-microbiome interactions and assist in biomarker discovery.
The field of pharmacomicrobiomics may benefit from machine learning to create precision therapies that consider microbiome-drug interactions.

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The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.

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Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders

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