Blueprint for AI-ready, standardized multi-omics in microbiome research

This Perspective argues that deciphering microbiome function requires coordinated, benchmarked, FAIR multi-omics workflows spanning metagenomics, metatranscriptomics, metaproteomics, and metabolomics. It reviews each layer’s strengths and limitations, highlights cross-omics integration challenges, and proposes a practical, tiered roadmap—foundational study design, integration and benchmarking, and ecosystem infrastructure—driven by community standards and open benchmarks to enable reproducible, interpretable, and AI-ready insights across diverse environments.