Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The National Microbiome Data Collaborative: enabling microbiome science

Nature Reviews Microbiology volume 18, pages 313–314 (2020)Cite this article

Subjects

To harness the potential of microbiome science across the broad range of relevant disciplines, new approaches to data infrastructure and transdisciplinary collaboration are necessary. The National Microbiome Data Collaborative (NMDC) is a new initiative to support microbiome data exploration and discovery through a collaborative, integrative data science ecosystem.

The cross-cutting nature of microbiome research in environmental sciences, health, agriculture, energy and in natural and built environments requires community coordination and the development of new solutions to tackle grand challenges in basic and applied research. The velocity of microbiome data generation has far outpaced infrastructure for collection, processing and distribution of these data in an effective and reproducible manner, aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles1. The research community has advocated for advanced tools, technologies and interdisciplinary research efforts2,3. A 2018 consensus strategic plan4 developed by 21 federal agencies further highlighted the need to support open and transparent data.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 3, 160018 (2016).

    Article  Google Scholar 

  2. Alivisatos, A. P. et al. A unified initiative to harness Earth’s microbiomes. Science 350, 507–508 (2015).

    Article  CAS  Google Scholar 

  3. Dubilier, N., McFall-Ngai, M. & Zhao, L. Microbiology: create a global microbiome effort. Nature 526, 631–634 (2015).

    Article  CAS  Google Scholar 

  4. U.S. Department of Energy Office of Scientific and Technical Information. Interagency Strategic Plan for Microbiome Research, FY 2018-2022, https://www.osti.gov/biblio/1471707-interagency-strategic-plan-microbiome-research-fy (2018).

  5. Buttigieg, P. L. et al. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J. Biomed. Semantics 7, 57 (2016).

    Article  Google Scholar 

  6. Yilmaz, P. et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotech. 29, 415–420 (2011).

    Article  CAS  Google Scholar 

  7. Mukherjee, S. et al. Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Res. 47, D649–d659 (2019).

    Article  CAS  Google Scholar 

  8. Stulberg, E. et al. An assessment of US microbiome research. Nat. Microbiol. 1, 15015 (2016).

    Article  CAS  Google Scholar 

  9. Proctor, L. et al. A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016. Microbiome 7, 31 (2019).

    Article  Google Scholar 

  10. Pylro, V. S. et al. Brazilian Microbiome Project: revealing the unexplored microbial diversity — challenges and prospects. Microb. Ecol. 67, 237–241 (2014).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Elisha M. Wood-Charlson, Shweta Deshpande, William D. Duncan, David Hays, Marcel Huntemann, Kayd Miller, T.B.K. Reddy, Jagadish Chandrabose Sundaramurthi, Pajau Vangay, Shane Canon, Kjiersten Fagnan, Christopher J. Mungall, Nigel J. Mouncey, Mary E. Maxon & Emiley A. Eloe-Fadrosh

  2. Pacific Northwest National Laboratory, Richland, WA, USA

    Anubhav, Deanna Auberry, Mark I. Borkum, Yuri E. Corilo, Mary Lipton, David Millard, Paul D. Piehowski, Samuel Purvine & Lee Ann McCue

  3. Oak Ridge National Laboratory, Oak Ridge, TN, USA

    Hannah Blanco, Ranjeet Devarakonda, Meghan Drake, Yaxing Wei, Bruce E. Wilson & Stanton Martin

  4. Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA

    Karen W. Davenport, Mark C. Flynn, Bin Hu, Po-E Li, Chien-Chi Lo, Migun Shakya & Patrick S. G. Chain

Authors
  1. Elisha M. Wood-Charlson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anubhav
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Deanna Auberry
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hannah Blanco
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mark I. Borkum
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yuri E. Corilo
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Karen W. Davenport
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Shweta Deshpande
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Ranjeet Devarakonda
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Meghan Drake
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. William D. Duncan
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Mark C. Flynn
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. David Hays
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Bin Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Marcel Huntemann
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Po-E Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Mary Lipton
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Chien-Chi Lo
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. David Millard
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Kayd Miller
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Paul D. Piehowski
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Samuel Purvine
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. T.B.K. Reddy
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Migun Shakya
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. Jagadish Chandrabose Sundaramurthi
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. Pajau Vangay
    View author publications

    You can also search for this author in PubMed Google Scholar

  27. Yaxing Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  28. Bruce E. Wilson
    View author publications

    You can also search for this author in PubMed Google Scholar

  29. Shane Canon
    View author publications

    You can also search for this author in PubMed Google Scholar

  30. Patrick S. G. Chain
    View author publications

    You can also search for this author in PubMed Google Scholar

  31. Kjiersten Fagnan
    View author publications

    You can also search for this author in PubMed Google Scholar

  32. Stanton Martin
    View author publications

    You can also search for this author in PubMed Google Scholar

  33. Lee Ann McCue
    View author publications

    You can also search for this author in PubMed Google Scholar

  34. Christopher J. Mungall
    View author publications

    You can also search for this author in PubMed Google Scholar

  35. Nigel J. Mouncey
    View author publications

    You can also search for this author in PubMed Google Scholar

  36. Mary E. Maxon
    View author publications

    You can also search for this author in PubMed Google Scholar

  37. Emiley A. Eloe-Fadrosh
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Emiley A. Eloe-Fadrosh.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Related links

Australian Microbiome Initiative: www.australianmicrobiome.com

Brazilian Microbiome Project: www.brmicrobiome.org

Center for Scientific Collaboration and Community Engagement: https://www.cscce.org

EMSL: https://search.emsl.pnnl.gov

FAIR Microbiome Implementation Network: https://www.go-fair.org/implementation-networks/overview/fair-microbiome

GOLD: https://gold.jgi.doe.gov

Metagenome workflows: https://github.com/microbiomedata/WorkflowPlanning

National Microbiome Data Collaborative: https://microbiomedata.org

NMDC Champion programme: https://microbiomedata.org/nmdc-champions

NMDC Code of Conduct: https://microbiomedata.org/nmdc-code-of-conduct

NMDC metadata schema: https://github.com/microbiomedata/nmdc-metadata

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wood-Charlson, E.M., Anubhav, Auberry, D. et al. The National Microbiome Data Collaborative: enabling microbiome science. Nat Rev Microbiol 18, 313–314 (2020). https://doi.org/10.1038/s41579-020-0377-0

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41579-020-0377-0

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing