Second funding phase proposal: NFDI4Microbiota – National Research Data Infrastructure for Microbiota Research

Abstract

Modern microbiological research generates vast quantities of data, particularly from high-throughput "omics" technologies. These datasets promise unprecedented insights into microbial diversity, function, and interactions, yet they are often deposited in unstructured formats with inadequate metadata, significantly hampering their discoverability, interoperability, and long-term reusability. Adding to this challenge is a long tail of subdomain-specific data types that typically lack a consistent structure. NFDI4Microbiota empowers microbiology researchers by transforming their research data into actionable knowledge that offers deeper insights into microbial life. The consortium makes data, software tools, analytical workflows, and machine-learning models FAIR (Findable, Accessible, Interoperable, and Reusable), ensuring they are AI-ready and openly available for efficient reuse. Key strategies include comprehensive training, developing and disseminating community-driven standards and best practices, fostering strong data stewardship, providing user-friendly data management tools and infrastructure, and promoting standardisation across the microbiology community. Building on our successful first funding phase, we will expand NFDI4Microbiota’s efforts in the next phase to enhance data accessibility and reuse while enabling AI applications. Our achievements and infrastructure from the first funding period provide a solid foundation for achieving an even greater impact across the microbiology research community and fostering a seamless flow of data. Community engagement remains vital: we will strengthen collaboration with existing stakeholders while actively reaching out to previously underrepresented groups, specifically researchers working on eukaryotic microbes such as fungi and protists, and we will work more closely with data-generating facilities to capture rich metadata early on. In addition, we will further strengthen our portfolio of services, databases, and analytical tools, ensuring that they are robust, interoperable, and tailored to evolving community needs. These enhancements will support a more comprehensive and inclusive data infrastructure for microbiological research. To help realise the One NFDI and EOSC vision of a coherent, sustainable, and collaborative research data ecosystem across all disciplines, NFDI4Microbiota will actively engage in cross-consortial initiatives, foster interoperability, and apply the unique perspectives of microbiological science to help shape the broader NFDI landscape.