Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Community Engagement Strategies of the National Microbiome Data Collaborative (NMDC)


Julia Kelliher1* ([email protected]), Alicia Clum3, Anastasiya Prymolenna2, Antonio Camargo3, Bin Hu1, Cameron Giberson2, Chien-Chi Lo1, Chris Mungall3, Donny Winston5, Elais Player Jackson1, Francie Rodriguez1, Grant Fujimoto2, Ingrid Ockert3, Jeff Baumes4, Kjiersten Fagnan3, Lee Ann McCue2, Marcel Huntemann3, Mark Flynn1, Mark Miller3, Michal Babinski1, Migun Shakya1, Mike Nagler4, Montana Smith2, Patrick Chain1, Patrick Kalita3, Paul Piehowski2, Po-E (Paul) Li1, Samuel Purvine2, Set Sarrafan3, Shane Canon3, Shreyas Cholia3, Simon Roux3, Sujay Patil3, Yan Xu1, Yuri Corilo2, and Emiley Eloe-Fadrosh3


1Los Alamos National Laboratory; 2Pacific Northwest National Laboratory; 3Lawrence Berkeley National Laboratory; 4Kitware, Inc.; and 5Polyneme LLC



The vision of the National Microbiome Data Collaborative (NMDC) is to connect data, people, and ideas to advance microbiome innovation and discovery. With this vision in mind, the NMDC seeks to support a findable, accessible, interoperable, and reusable (FAIR) microbiome data sharing network through infrastructure, data standards, and community building that addresses pressing challenges in environmental sciences. The NMDC engagement strategy focuses on promoting a collaborative ecosystem for diverse microbiome researchers and implementing community feedback in all of the NMDC efforts and products.


The NMDC is a multi-national laboratory initiative focused on advancing innovation and discovery in the field of microbiome science through the project’s development of products and tools for the environmental microbiome research community (Wood-Charlson et al. 2020). The NMDC provides the community with three products: (1) The Submission Portal, (2) The Data Portal (Eloe-Fadrosh et al. 2022), and (3) NMDC EDGE, each aimed at making multiomics microbiome data FAIR. Each of these products was designed to specifically address the larger research community’s specific needs and wants. The NMDC team implements recommendations and insights gleaned from usability testing and community feedback to continuously improve products. The team routinely engages with microbiome researchers to discuss how they want the NMDC products to look and operate, as well as understand what new functionality would benefit future research. In addition, the NMDC communicates and engages with many types of stakeholders, including funding agencies, publishers, institutions, programs, projects, and individual scientists. As part of these collaborative efforts, the NMDC hosts and co-hosts workshops (Vangay et al. 2021), webinars, presentations, panel discussions, and other events aimed at spreading awareness of and lowering barriers to adoption of FAIR principles in microbiome research and data generation. The NMDC Ambassador program allows early career researchers to host some of these events, thus expanding the overall reach of the content and training materials, while providing the Ambassadors with valuable experiences and career opportunities. The NMDC Champions program brings together microbiome researchers from diverse backgrounds to contribute to the NMDC (e.g., by beta-testing the NMDC products, co-authoring publications with the NMDC team, providing feedback, etc.). The NMDC will continue to prioritize community engagement as the products and network grow.


Eloe-Fadrosh, E. A., et al. 2022. “The National Microbiome Data Collaborative Data Portal: An Integrated Multi-Omics Microbiome Data Resource,” Nucleic Acids Research 50(D1), D828–36. DOI:10.1093/nar/gkab990.

Vangay, P., et al. 2021. “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-on Activities,” mSystems 6, e01194-20. DOI:10.1128/mSystems.01194-20.

Wood-Charlson, E. M., et al. 2020. “The National Microbiome Data Collaborative: Enabling Microbiome Science,” Nature Reviews Microbiology 18, 313–14. DOI:10.1038/s41579-020-0377-0.

Funding Information

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