A Guide to Human Microbiome Data Repositories

This review chronicles the evolution of human microbiome research, tracing its trajectory from early descriptive studies to the current era of large multi-omics repositories. Technological advancements, such as high-throughput 16S rRNA sequencing and whole metagenome shotgun sequencing, have shifted the field from cataloguing microbial inhabitants to understanding their functional roles and interactions with the human host. The primary aim of this document is to offer researchers a concise and accessible guide to the major human microbiome projects and the repositories that store their data, outlining the data flow starting from sample collection, in a simple, comprehensive way. We synthesize the contributions of key international projects that have shaped the field and provide a full overview of the repositories that store human microbiome data, clarifying their scope, structure, and utility for different research needs. Looking ahead, the field is moving toward multi-omics integration, AI-driven analysis, and globally inclusive sampling. Future progress will require advancing sequencing technologies while building infrastructures that are capable of handling increasingly complex data.