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An assessment of US microbiome research


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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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.

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Authors and Affiliations



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).

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