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An assessment of US microbiome research

Nature Microbiology volume 1, Article number: 15015 (2016) Cite this article

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Abstract

Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using ’omics technologies. Single pathogen, single strain and culture-based studies were not included, except symbiosis studies that served as models for more complex communities. Fourteen governmental organizations participated in the data call. The analysis examined three broad research themes, eight environments and eight microbial categories. Human microbiome research was larger than any other environment studied, and the basic biology research theme accounted for half of the total research activities. Computational biology and bioinformatics, reference databases and biorepositories, standardized protocols and high-throughput tools were commonly identified needs. Longitudinal and functional studies and interdisciplinary research were also identified as needs. This study has implications for the funding of future microbiome research, not only in the United States but beyond.

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Figure 1: Microbiome research by ecosystem.
Figure 2: Microbiome research by theme and microbe.

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Acknowledgements

The Committee acknowledges the efforts of colleagues in our respective agencies who worked to meet the six-week data call deadline. The authors acknowledge the earlier efforts of the trans-NIH Microbiome Working Group (TMWG), whose FY10-12 portfolio analysis formed the basis of the approach and format for this data call.

Author information

Authors and Affiliations

  1. Office of Science and Technology Policy, Executive Office of the President, Eisenhower Executive Office Building, 1650 Pennsylvania Ave. NW, Washington, 20504, DC, USA

    Elizabeth Stulberg

  2. United States Department of Agriculture, Plant Health, Crop Production and Protection, Agricultural Research Service, 5601 Sunnyside Ave., Beltsville, 20705, Maryland, USA

    Deborah Fravel

  3. Department of Health and Human Services, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, 20892, Maryland, USA

    Lita M. Proctor & Jonathan LoTempio

  4. Department of Health and Human Services, Office of Disease Prevention, National Institutes of Health, 6100 Executive Boulevard, Rockville, 20852, Maryland, USA

    David M. Murray

  5. Department of Defense, Office of Naval Research, 875 N. Randolph Street, Arlington, 22205-1995, Virginia, USA

    Linda Chrisey

  6. United States Environmental Protection Agency, Office of Research & Development, 26 West Martin Luther King Drive, Cincinnati, 45268, Ohio, USA

    Jay Garland

  7. Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic & Meteorological Laboratory, National Oceanic and Atmospheric Administration, 4301 Rickenbacker Causeway, Miami, 33149, Florida, USA

    Kelly Goodwin

  8. Stationed at NOAA, Southwest Fisheries Science Center, La Jolla Shores Drive, La Jolla, 92037, California, USA

    Kelly Goodwin

  9. US Department of Energy, Office of Biological & Environmental Research, 1000 Independence Ave. SW, Washington, 20585, DC, USA

    Joseph Graber

  10. Department of the Interior, Ecosystems Mission Area, United States Geological Survey, 12201 Sunrise Valley Drive, Reston, 20192, Virginia, USA

    M. Camille Harris

  11. Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, 20899, Maryland, USA

    Scott Jackson

  12. Physiological and Structural Systems Cluster, Integrative Organismal Systems, National Science Foundation, 4201 Wilson Boulevard, Arlington, 22230, Virginia, USA

    Michael Mishkind

  13. NASA Life and Physical Sciences, Human Exploration and Operations Mission Directorate, National Aeronautics and Space Administration, 300 E Street SW, Washington, 20546, DC, USA

    D. Marshall Porterfield

  14. Office of Agriculture, Research and Policy, Bureau for Food Security, US Agency for International Development, 1300 Pennsylvania Ave. NW, Washington, 20523, DC, USA

    Angela Records

Authors
  1. Elizabeth Stulberg
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  2. Deborah Fravel
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  3. Lita M. Proctor
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  4. David M. Murray
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  5. Jonathan LoTempio
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  6. Linda Chrisey
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  7. Jay Garland
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  8. Kelly Goodwin
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  9. Joseph Graber
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  10. M. Camille Harris
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  11. Scott Jackson
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  12. Michael Mishkind
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  14. Angela Records
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Contributions

E.S., D.F., L.P. and D.M. conceived the study. All authors jointly planned the data collection effort. All authors except E.S. and J.L. managed the data collection at their agency or department and provided their data to the central database. E.S. and J.L. conducted the analysis, and L.P. and E.S. prepared the initial draft of the manuscript. All authors revised the manuscript and agreed on the final version.

Corresponding author

Correspondence to Elizabeth Stulberg.

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Competing interests

All authors are federal employees and the preparation of this manuscript was done as part of their official duties.

Supplementary information

Supplementary Data 1

An interactive version of the FTACMM Data Call spreadsheet (XLSX 118 kb)

Supplementary Data 2

The logic flow for the FTACMM drop down menu. (XLSX 10 kb)

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Stulberg, E., Fravel, D., Proctor, L. et al. An assessment of US microbiome research. Nat Microbiol 1, 15015 (2016). https://doi.org/10.1038/nmicrobiol.2015.15

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