Transformer Models, Graph Networks, and Generative AI in Gut Microbiome Research: A Narrative Review

<h4>Background</h4>The rapid advancement in artificial intelligence (AI) has fundamentally reshaped gut microbiome research by enabling high-resolution analysis of complex, high-dimensional microbial communities and their functional interactions with the human host.<h4>Objective</h4>This narrative review aims to synthesize recent methodological advances in AI-driven gut microbiome research and to evaluate their translational relevance for therapeutic optimization, personalized nutrition, and precision medicine.<h4>Methods</h4>A narrative literature review was conducted using PubMed, Google Scholar, Web of Science, and IEEE Xplore, focusing on peer-reviewed studies published between approximately 2015 and early 2025. Representative articles were selected based on relevance to AI methodologies applied to gut microbiome analysis, including machine learning, deep learning, transformer-based models, graph neural networks, generative AI, and multi-omics integration frameworks. Additional seminal studies were identified through manual screening of reference lists.<h4>Results</h4>The reviewed literature demonstrates that AI enables robust identification of diagnostic microbial signatures, prediction of individual responses to microbiome-targeted therapies, and design of personalized nutritional and pharmacological interventions using in silico simulations and digital twin models. AI-driven multi-omics integration-encompassing metagenomics, metatranscriptomics, metabolomics, proteomics, and clinical data-has improved functional interpretation of host-microbiome interactions and enhanced predictive performance across diverse disease contexts. For example, AI-guided personalized nutrition models have achieved AUC exceeding 0.8 for predicting postprandial glycemic responses, while community-scale metabolic modeling frameworks have accurately forecast individualized short-chain fatty acid production.<h4>Conclusions</h4>Despite substantial progress, key challenges remain, including data heterogeneity, limited model interpretability, population bias, and barriers to clinical deployment. Future research should prioritize standardized data pipelines, explainable and privacy-preserving AI frameworks, and broader population representation. Collectively, these advances position AI as a cornerstone technology for translating gut microbiome data into actionable insights for diagnostics, therapeutics, and precision nutrition.