Focuses of the National Microbiome Data Collaborative


Alicia Clum1* ([email protected]), Anastasiya Prymolenna2, Antonio Camargo1, Bin Hu2, Cameron Giberson2, Chien-Chi Lo3, Chris Mungall1, Donny Winston5, Elais Player Jackson3, Francie Rodriguez3, Grant Fujimoto2, Ingrid Ockert1, Jeff Baumes4, Julia Kelliher3, Kjiersten Fagnan1, Lee Ann McCue2, Marcel Huntemann1, Mark Flynn3, Mark Miller1, Michal Babinski3, Migun Shakya3, Mike Nagler4, Montana Smith2, Patrick Chain3, Patrick Kalita1, Paul Piehowski2, Po-E (Paul) Li3, Samuel Purvine2, Set Sarrafan1, Shane Canon1, Shreyas Cholia1, Simon Roux1, Sujay Patil1, Yan Xu3, Yuri Corilo2, Emiley Eloe-Fadrosh1


1Lawrence Berkeley National Laboratory, Berkeley, California; 2Pacific Northwest National Laboratory, Richland, Washington; 3Los Alamos National Laboratory, Los Alamos, New Mexico; 4Kitware Inc., Clifton Park, NY; 5Polyneme LLC, New York, NY



The National Microbiome Data Collaborative (NMDC) is committed to providing findable, accessible, interoperable, and reusable (FAIR) multiomics microbiome data. This is accomplished through the three key NMDC products that are openly available to the research community: the submission portal (, the data portal (; Eloe-Fadrosh et al. 2022), and NMDC EDGE ( The NMDC Submission Portal provides users a place to contribute sample metadata in a standardized manner with in-sheet validation to ensure machine readability and findability. The Data Portal consumes this metadata and presents search tools to find and access information about the research studies and data generated from the samples. The Data Portal also provides links to the associated omics data processed through NMDC’s standardized bioinformatics workflows. NMDC EDGE is a user-friendly interface for NMDC standardized bioinformatics workflows. These three NMDC products are built specifically with the BER research community in mind and refined through a process of continual collaboration based on user-focused feedback. Leveraging each of the NMDC products enables environmental microbiome researchers to adhere to FAIR data principles, thus expanding potential research questions, comparisons, and scientific discovery.


Eloe-Fadrosh, E.A., et al. 2022. “The National Microbiome Data Collaborative Data Portal: An Integrated Multiomics Microbiome Data Resource,” Nucleic Acids Research 50(D1), D828–D836. DOI:10.1093/nar/gkab990.

Funding Information

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