Decoding host–microbiome interactions through integrative multi-omics and artificial intelligence: from biological mechanisms to predictive modelling

Abstract

The mutual communication between the human host and its microbiome plays a fundamental role in maintaining metabolic and immunological homeostasis. Disruptions in this delicate ecosystem are heavily linked to severe pathologies like inflammatory bowel disease (IBD), metabolic syndromes, and cancer. Whilst traditional single-omics approaches offer limited taxonomic snapshots, multi-omics strategies are bridging the gap by mapping the complex, multi-layered networks driving host-microbe interactions. However, integrating these highly dimensional, heterogeneous datasets creates significant computational bottlenecks. Artificial Intelligence (AI), spanning machine learning and deep learning architectures, has emerged as a critical catalyst to resolve this crisis. AI transforms complex data into predictive models for early diagnosis, clinical biomarker discovery, and personalised therapeutics. Despite persistent hurdles in model generalisation and data standardisation, the convergence of multi-omics and AI is actively driving the future of precision medicine.