Polybiome Systems Medicine: Conceptual Architecture, Methodological Foundations, and Translational Applications — An Open Science Reference Framework

This project establishes Polybiome Systems Medicine as a foundational Open Science reference framework, redefining the human organism not as a singular host, but as an emergent biological consortium. By employing multi-scalar systems ontologies, the framework integrates host genomics/epigenomics, the multi-kingdom microbiota, metabolic-nutritional networks, and the environmental exposome into a unified, AI-driven temporal architecture. Distinct from traditional preprints or clinical protocols, this document serves as a Methodological and Translational Reference. It is engineered to provide a stable, citable infrastructure for: Institutional Governance: Aligning health policy with systems-level biological realities. Systems Medicine Pedagogy: Serving as a roadmap for advanced research and interdisciplinary education. Computational Biology: Defining AI-ready pipelines for high-dimensional multi-omics integration. Predictive Diabetology: Implementing models like the NexDi algorithm for precision reclassification. Bio-Sovereignty: Providing ethical blueprints for the protection of national biological assets. By adhering to Open Science principles, this framework ensures transparency, citability, and continuous versioning. It stands as a definitive reference point for stakeholders—researchers, clinicians, and policymakers—engaged in the transition toward anticipatory, AI-driven precision health. The original, peer-reviewed version of this document is officially published and archived on Zenodo. REYED, R. M. (2026). Polybiome Systems Medicine: Conceptual Architecture, Methodological Foundations, and Translational Applications — Volume I: Vision and Foundational Methodology (0.1). Zenodo. https://doi.org/10.5281/zenodo.18294835