Orion Microbiome Database: mapping constellations in the microbiome universe

Abstract Background Publicly available microbiome sequencing data have grown rapidly in scale and diversity, but secondary use remains limited by fragmentation across repositories, inconsistent annotations, heterogeneous processing pipelines, and incomplete metadata. These barriers complicate cross-study comparisons and restrict the reproducibility of large-scale microbiome research. Objective The Orion Microbiome Database was developed to overcome these challenges by providing a standardized, accessible, and reproducible resource for the integration and analysis of whole-genome shotgun (WGS) microbiome datasets. Methods Orion aggregates raw metagenomic datasets from public repositories and harmonizes them into computed microbial profiles using automated and transparent analysis pipelines. Metadata are curated to ensure consistency and enable systematic cross-cohort comparisons. The platform provides interactive tools for data exploration, visualization, and downstream analysis, reducing redundancies in data preprocessing and lowering the barrier for both novice and expert users. Beyond research applications, Orion also serves as an educational resource, enabling microbiome data exploration in classroom settings. Conclusion By unifying fragmented sequencing resources into a reproducible framework, Orion accelerates microbiome discovery, supports scalable cross-study investigations, and fosters integration of microbiome science into teaching and training. This database has the potential to serve as a model for future large-scale, community-driven platforms in microbiome research.