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Cohort-based learning for microbiome research community standards

Nature Microbiology volume 8, pages 751–753 (2023)Cite this article

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In the past decade, microbiome researchers have produced a wealth of sequence data and associated microbial outputs and activity1. Most microbiome studies to date have analysed microbiomes in order to answer a specific research question, with little emphasis placed on data reusability. However, increasing microbiome data reuse would result in a better return on investments and an increase in accessibility to microbiome science for researchers unable to generate their own microbiome data. It may also enable researchers to address scientific questions beyond the scope of the original study2. Recognizing these advantages, the scientific community has repeatedly advocated for findable, accessible, interoperable and reusable (FAIR) data3. We launched the National Microbiome Data Collaborative (NMDC) Ambassador Program in April 2021 to increase FAIR data adoption and metadata stewardship among microbiome researchers. Herein, we provide information and insights regarding the implementation of a community learning model to assist in the advancement of other iterations of this type of programme.

The campaign for FAIR data advocates for sufficient metadata (for example, geographic location, sampling date, host information, and so on) to be available for microbiome datasets, because the utility and reusability of data sharply decrease when crucial metadata fields are missing, insufficient or improperly formatted4,5. Training events, ideally with a practical or hands-on component, are essential to increase recognition and adoption of metadata standards.

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Fig. 1: The selection of the pilot cohort of NMDC Ambassadors, the locations of their affiliated institutions and the quantitative impact of the Ambassador Program.

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Author information

Authors and Affiliations

  1. Los Alamos National Laboratory, Los Alamos, NM, USA

    Julia M. Kelliher, Karen W. Davenport & Francisca E. Rodriguez

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

    Marisa Rudolph, Pajau Vangay, Ingrid Ockert, Elisha M. Wood-Charlson & Emiley A. Eloe-Fadrosh

  3. Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Arwa Abbas

  4. Colorado State University, Fort Collins, CO, USA

    Mikayla A. Borton

  5. Pennsylvania State University, State College, PA, USA

    Emily R. Davenport

  6. Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA

    Natalia G. Erazo

  7. Northern Arizona University, Flagstaff, AZ, USA

    Chloe Herman

  8. Oregon Health and Science University, Portland, OR, USA

    Lisa Karstens

  9. Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA

    Brandon Kocurek

  10. Scripps Research, La Jolla, CA, USA

    Holly L. Lutz

  11. Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA

    Kevin S. Myers

  12. Center for Scientific Collaboration and Community Engagement, Oakland, CA, USA

    Camille Santistevan & Lou Woodley

  13. Woods Hole Oceanographic Institution, Falmouth, MA, USA

    Jaclyn K. Saunders

  14. University of Georgia, Athens, GA, USA

    Jaclyn K. Saunders

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

    Montana L. Smith

  16. National Cancer Institute, Bethesda, MD, USA

    Emily Vogtmann

  17. Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA

    Amanda Windsor

Authors
  1. Julia M. Kelliher
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  2. Marisa Rudolph
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  3. Pajau Vangay
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  4. Arwa Abbas
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  5. Mikayla A. Borton
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  6. Emily R. Davenport
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  7. Karen W. Davenport
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  8. Natalia G. Erazo
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  9. Chloe Herman
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  10. Lisa Karstens
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  11. Brandon Kocurek
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  12. Holly L. Lutz
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  13. Kevin S. Myers
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  14. Ingrid Ockert
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  15. Francisca E. Rodriguez
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  16. Camille Santistevan
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  17. Jaclyn K. Saunders
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  18. Montana L. Smith
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  19. Emily Vogtmann
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  20. Amanda Windsor
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  21. Elisha M. Wood-Charlson
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  22. Lou Woodley
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  23. Emiley A. Eloe-Fadrosh
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Contributions

J.M.K. and E.A.E.-F. conceptualized and wrote the majority of the manuscript with substantial contributions from M.R. and P.V. A.A., M.A.B., E.R.D., N.G.E., C.H., L.K., B.K., H.L.L., K.S.M., J.K.S., E.V. and A.W. were the Ambassadors from this pilot cohort and contributed to the content of the manuscript. C.S. and L.W. contributed to the programme and synthesis of feedback and results. P.V. also ran the Ambassador Program during the pilot cohort and K.W.D., I.O., F.E.R., M.L.S. and E.M.W.-C. contributed to running the Ambassador Program, creating training materials and editing the manuscript. All authors reviewed and approved the manuscript.

Corresponding authors

Correspondence to Julia M. Kelliher or Emiley A. Eloe-Fadrosh.

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The authors declare no competing interests.

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Kelliher, J.M., Rudolph, M., Vangay, P. et al. Cohort-based learning for microbiome research community standards. Nat Microbiol 8, 751–753 (2023). https://doi.org/10.1038/s41564-023-01361-7

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