Consensus Statement

An assessment of US microbiome research

  • Nature Microbiology 1, Article number: 15015 (2016)
  • doi:10.1038/nmicrobiol.2015.15
  • Download Citation
Received:
Accepted:
Published online:

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.

  • Subscribe to Nature Microbiology for full access:

    $59

    Subscribe

Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.

References

  1. 1.

    et al. Genomic analysis of uncultured marine viral communities. Proc. Natl Acad. Sci. USA 99, 14250–14255 (2002).

  2. 2.

    et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004).

  3. 3.

    et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006).

  4. 4.

    Fast-Track Action Committee on Mapping the Microbiome (National Science and Technology Council, 2015);

  5. 5.

    , & Unraveling plant–microbe interactions: can multi-species transcriptomics help? Trends Biotechnol. 30, 177–184 (2012).

  6. 6.

    , , & Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome. Mol. Ecol. 23, 1571–1583 (2014).

  7. 7.

    The virome in mammalian physiology and disease. Cell 157, 142–150 (2014).

  8. 8.

    & Rising to the challenge: accelerated pace of discovery transforms marine virology. Nature Rev. Microbiol. 13, 147–159 (2015).

  9. 9.

    Move over bacteria! Viruses make their mark as mutualistic microbial symbionts. J. Virol. 89, 6532–6535 (2015).

  10. 10.

    et al. Densovirus associated with sea-star wasting disease and mass mortality. Proc. Natl Acad. Sci. USA 111, 17278–17283 (2014).

  11. 11.

    et al. Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation. FEMS Micro. Ecol. (2015).

  12. 12.

    et al. Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases. ISME J. (2015).

  13. 13.

    et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012).

  14. 14.

    et al. Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation. J. Exp. Med. 209, 903–911 (2012).

  15. 15.

    et al. Complete suppression of the gut microbiome prevents acute graft-versus-host disease following allogenic bone marrow transplantation. PLoS ONE 9, e105706 (2014).

  16. 16.

    & Microbiome in human immunodeficiency virus infection. Clin. Lab. Med. 34, 733–745 (2014).

  17. 17.

    et al. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64, 807–838 (2013).

  18. 18.

    et al. Towards a global platform for linking soil biodiversity data. Front. Ecol. Evol. 3, 91 (2015).

  19. 19.

    et al. Key role of symbiotic N2 fixation in tropical forest secondary succession. Nature 502, 224–227 (2013).

  20. 20.

    & The microbial ecology of permafrost. Nature Rev. Microbiol. 12, 414–425 (2014).

  21. 21.

    et al. Temperature sensitivity of soil respiration rates enhanced by microbial community response. Nature 513, 81–84 (2014).

  22. 22.

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

  23. 23.

    The NIH Human Microbiome Project, phase one;

  24. 24.

    The EC MetaHIT programme;

  25. 25.

    The Canadian Human Microbiome Initiative;

  26. 26.

    The Irish ELDERMET programme;

  27. 27.

    Microbiology: the inside story. Nature 453, 578–579 (2008).

  28. 28.

    The International Human Microbiome Consortium;

  29. 29.

    The NIH Human Microbiome Project, phase two;

  30. 30.

    The EC ‘My New Gut’ programme;

  31. 31.

    The Irish APC Microbiome Institute;

  32. 32.

    The EC ‘Metagenopolis’ programme;

  33. 33.

    The Canadian ‘Environment, Gene and Chronic Diseases’ programme;

  34. 34.

    The Canadian ‘Natural Resources and the Environment: Sector Challenges – Genomic Solutions’ programme;

  35. 35.

    The EC ‘Joint Action Intestinal Microbiomics’ programme;

  36. 36.

    The NSF Microbial Observatories and Microbial Interactions and Processes programme;

  37. 37.

    The NSF Microbial Genome Sequencing Program;

  38. 38.

    The International Census on Marine Microbes;

  39. 39.

    The Gordon and Betty Moore Foundation Marine Microbiology Initiative;

  40. 40.

    TerraGenome, the International Soil Metagenome Sequencing Consortium;

  41. 41.

    The DOE Microbial Carbon Cycle programme;

  42. 42.

    , & The Earth Microbiome Project: successes and aspirations. BMC Biol. 12, 69 (2014).

  43. 43.

    et al. The ocean sampling day consortium. GigaScience 4, 66 (2015).

Download references

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

Affiliations

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

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

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

    • Lita M. Proctor
    •  & Jonathan LoTempio
  4. Office of Disease Prevention, National Institutes of Health, Department of Health and Human Services, 6100 Executive Boulevard, Rockville, Maryland 20852, USA

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

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

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

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

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

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

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

    • Scott Jackson
  12. Physiological and Structural Systems Cluster, Integrative Organismal Systems, National Science Foundation, 4201 Wilson Boulevard, Arlington, Virginia 22230, 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, DC 20546, 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, DC 20523, USA

    • Angela Records

Authors

  1. Search for Elizabeth Stulberg in:

  2. Search for Deborah Fravel in:

  3. Search for Lita M. Proctor in:

  4. Search for David M. Murray in:

  5. Search for Jonathan LoTempio in:

  6. Search for Linda Chrisey in:

  7. Search for Jay Garland in:

  8. Search for Kelly Goodwin in:

  9. Search for Joseph Graber in:

  10. Search for M. Camille Harris in:

  11. Search for Scott Jackson in:

  12. Search for Michael Mishkind in:

  13. Search for D. Marshall Porterfield in:

  14. Search for Angela Records in:

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.

Competing interests

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

Corresponding author

Correspondence to Elizabeth Stulberg.

Supplementary information

Excel files

  1. 1.

    Supplementary Data 1

    An interactive version of the FTACMM Data Call spreadsheet

  2. 2.

    Supplementary Data 2

    The logic flow for the FTACMM drop down menu.