A collaborative partnership united by a single vision

Our Story

The NMDC enables the microbiome research community to decode the molecular underpinnings of fundamental biological processes, and ultimately, drive transformational discoveries.

In 2016, the White House Office of Science and Technology Policy (OSTP), in collaboration with federal agencies and private-sector stakeholders, launched the National Microbiome Initiative focused on three main priorities: supporting interdisciplinary research, developing platform technologies, and expanding the microbiome workforce. This spurred a call to action for microbiome data science, led by Nikos Kyrpides, Natalia Ivanova, and Emiley Eloe-Fadrosh. A small workshop convened in early 2017 at the Department of Energy’s Joint Genome Institute focused on developing a vision for microbiome data science to address gaps in existing infrastructure.  

Working from a collaborative vision for a microbiome data infrastructure that was outlined at the workshop, an open-invitation town hall was organized at the 2017 ASM Microbe conference to gauge support and solicit input from the microbiome research community. Stakeholders from all facets of microbiome science filled the standing-room-only meeting and signaled a collective eagerness for concerted data infrastructure solutions. In November 2017, a stakeholder workshop hosted by the American Society for Microbiology brought together representatives from academia, industry, government, and philanthropic funding agencies to conceptualize the National Microbiome Data Collaborative (NMDC). These efforts serve as the foundation of a community-driven national effort aimed to develop standards, processes, and infrastructure for an integrated microbiome data ecosystem.

Following these program development activities, the FY19 Energy and Water Appropriations Bill included $10 million to “begin establishment of a national microbiome database.” In January 2019, Berkeley Lab was formally tasked by the DOE Office of Biological and Environmental Research to develop a pilot NMDC as a non-competed program. The NMDC was initiated in July 2019 as a 27-month pilot project led by Berkeley Lab, in partnership with Los Alamos National Laboratory (LANL), Pacific Northwest National Laboratory (PNNL) and Oak Ridge National Laboratory (ORNL).

Enabling inclusive and interdisciplinary environmental microbiome science by connecting data, people, and ideas.

The long-term vision of the NMDC is to support microbiome data exploration through a sustainable data discovery platform that promotes open science and shared-ownership across a broad and diverse community of researchers, funders, publishers, societies, and other Collaborators (see the NMDC Code of Conduct). To support this shared long-term scientific vision of microbiome science, the NMDC team works with the community to iteratively develop and pilot an integrated, open source microbiome science gateway that leverages existing resources and enables comprehensive access to multidisciplinary microbiome data and standardized, reproducible data products.


One vision united by two strategic priorities
Strategic Priority: Infrastructure
  • Standards with expert curation
  • FAIR principles
  • Gold-standard pipelines
  • Streamlined data search & access
Strategic Priority: Engagement
  • Research Teams
  • Funders
  • Publishers
  • Societies


This work is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).


How to cite the NMDC:

E. M. Wood-Charlson, Anubhav, D. Auberry, H. Blanco, M. I. Borkum, Y. E. Corilo, K. W. Davenport, S. Deshpande, R. Devarakonda, M. Drake, W. D. Duncan, M. C. Flynn, D. Hays, B. Hu, M. Huntemann, P.-E. Li, M. Lipton, C.-C. Lo, D. Millard, K. Miller, P. D. Piehowski, S. Purvine, T. B. K. Reddy, M. Shakya, J. C. Sundaramurthi, P. Vangay, Y. Wei, B. E. Wilson, S. Canon, P. S. G. Chain, K. Fagnan, S. Martin, L. A. McCue, C. J. Mungall, N. J. Mouncey, M. E. Maxon, E. A. Eloe-Fadrosh, The National Microbiome Data Collaborative: enabling microbiome science. Nature Reviews Microbiology 18, 313-314 (2020). doi: 10.1038/s41579-020-0377-0

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