Advancing microbiome science together
Celebrating Seven Years of NMDC: Program Conclusion and Next Steps
Dear Microbiome Community,
The NMDC program initiated in 2019 by the Department of Energy (DOE) Biological and Environmental Research (BER) program set out to address a critical challenge in microbiome research: converting fragmented multi-omics data into findable, accessible, interoperable, and reusable scientific assets. Today, we are writing to share a significant transition milestone for the program. BER intends to integrate core NMDC functionalities directly into the newly initiated BER program DOE-BRIDGE.
As part of BER’s bold new strategic vision to build a unified, comprehensive biological data ecosystem, the standalone NMDC program will be concluding. However, this is not an end to the resources you rely on. Critical multi-omics data generated and curated through the NMDC will remain available through DOE-BRIDGE. The BRIDGE Scientific Data Ecosystem serves as the coordinating architecture—seamlessly linking BER User Facility data and services to the American Science Cloud (AmSC). Consistent with BER priorities, the broader scientific community will experience no disruption in accessing NMDC’s data services in the short-term, please review the FAQs that address each service in more detail. Data generated by the NMDC will be preserved in the BRIDGE infrastructure.
Reflecting on Seven Years of Impact
The NMDC has served as a pioneer for FAIR (Findable, Accessible, Interoperable, Reusable) data stewardship in the microbial sciences. Together with you, we have built a legacy of incredible accomplishments, including:
- The NMDC Data and Submission Portals: We successfully built robust platforms that unified diverse multi-omics data—including metagenomics, metatranscriptomics, metaproteomics, and metabolomics—into a searchable, public index that has accelerated discoveries across microbiome and environmental science. Our growth includes 153.7 TB of multi-omics data spanning 29,364 unique environmental samples and 208 formal submissions, with a digital reach of over 1,472 ORCiD-authenticated user accounts, 59,588 website visitors, over 300 publications and research outputs citing the NMDC, and 664 direct insights gathered from user research participants.
- Gold-Standard Metadata Schemas: We spearheaded community-driven metadata standards, aligning with the international MIxS standard, to ensure that every sample uploaded is rich in context, standardized, and machine-readable.
- Standardized Bioinformatics Workflows: We made BER high-performance computational pipelines accessible, allowing researchers to run standardized workflows on leading national lab computing resources.
- Community and education: Advanced community engagement through the Microbiome Certificate Program, early-career training via Ambassador and Champions initiatives, and the development of globally adopted STREAMS guidelines for standardized microbiome research reporting.
A Heartfelt Thank You
This journey would have been entirely impossible without the passionate ecosystem of collaborators who believed in the power of data stewardship. We want to express our deepest gratitude to:
- Our Core Team: Whose tireless work, brilliant engineering, and scientific vision built the very portals, workflows, and standards that are now being integrated to strengthen the broader BER ecosystem.
- Our Ambassadors and Champions: Who served as our grassroots advocates, dedicating their time to teaching data stewardship, hosting workshops, and leading metadata standards training across institutions worldwide.
- Our Scientific Advisory Board (SAB): Whose strategic guidance, oversight, and expert critiques kept our program centered, scientifically rigorous, and focused on community needs.
- DOE’s BER Program: For their vision and sustained investment over the past seven years, which made building this pioneering microbiome data stewardship infrastructure possible.
- The Entire Scientific Community: Who embraced our platform, shared their invaluable feedback, contributed data, and continuously championed the fundamental truth that open, accessible, and well-curated data is the bedrock of modern scientific advancement.
What’s Next?
We welcome you to review our FAQs page that describes in more detail the NMDC’s transition, our timelines, and what services will be maintained.
Thank you for seven incredible years of collaboration.
With our deepest gratitude,
The NMDC Leadership Team
Community-driven data infrastructure
The NMDC is tackling existing gaps in microbiome science through distributed data infrastructure and linked data technologies. Our components — the Submission Portal,the Data Portal, and API — are driven by community needs. They support data, information, knowledge sharing, and access.
Interdisciplinary community
The NMDC seeks to connect and engage the microbiome community to unlock new possibilities in microbiome data science. Our User Research program ensures we develop resources that advance microbiome science. We support participation in data curation, discovery, and analytical processes through active partnerships among the research community.
Advancing how scientists create, use, and reuse microbiome data
Data standards with expert curation
Map existing ontologies and standard vocabularies to the rich contextual metadata used to describe sample collection and processing.
Use ontology mapping tools and curation resources to enable automated annotation of standardized metadata to adhere to the FAIR principles.
Standardized bioinformatics workflows
Develop microbiome workflows for metagenomes, metatranscriptomes, metaproteomes, and metabolomics data processing leveraging high performance compute (HPC) systems.
Generate and integrate interoperable and reusable microbiome data from data providers.
Data integration and access
Iteratively develop a graphical web-based interface that streamlines search, data exploration, and discovery.
Provide access to FAIR multidisciplinary data and standardized, reproducible data products for comparative analyses.
Engagement and partnerships
Establish support for open science and FAIR microbiome data across research teams and science programs.
Partner with publishers, funders, and scientific societies and consortiums to incentivize data sharing and reuse.
Building a world where data is FAIR
Findable
Ensuring all data registered within the NMDC ecosystem is human and machine readable
Accessible
Identifying datasets that are available, including any authentication and authorization requirements
Interoperable
Providing provenance, metadata, and uniformly processed data that can be exchanged across resources
Reusable
Enabling download of data, data products, and workflows for analyses and sharing
