Recent advances in high-throughput microbiome profiling have generated expansive data sets that offer unprecedented opportunities to investigate the role of microbes in human health. However, the complexity and high dimensionality of these data present significant analytical challenges that often exceed the capabilities of traditional computational methods. Artificial intelligence (AI), encompassing both classical machine learning and modern deep learning approaches, has emerged as a powerful solution to these challenges. In this review, we systematically explore AI-driven methodologies in microbiome research, including clustering algorithms, dimensionality reduction techniques, convolutional and recurrent neural networks, and emerging large language models. We assess how these approaches enable the extraction of meaningful biological patterns from complex microbial data from a multiscale perspective, facilitating insights into community dynamics, host–microbe interactions and functional genomics. Additionally, we explore the transformative impact of AI on translational applications across both academic research and real-world clinical settings, including disease diagnostics, therapeutic development and precision microbiome engineering. By critically evaluating the current capabilities and limitations of AI in this context, this review aims to chart a path forward for the integration of AI into microbiome research, ultimately accelerating innovations in personalised medicine and deepening our understanding of host–microbiome relationships.
Tian et al. (2025) studied this question.