PERSPECTIVE omiotation plator omingnh 5. 6 of biomolecules from highly diverse and complex sample matrices. such as soil,sediments and the human gut;assembly of complete genomes rather er speed,throug 9. 7 ly o meeting the high computational RAMrequirements ford assembly of large metagenomes and metatranscriptomes 10. 1. throughput loping sta Is to data cl and m 28136.36519 ofabricated high-density research.Recently,the White House Office of Science and ing using even faster 034543 lations and inaddition to thedevelopment of bioinformatics programs tha obiom oma varicty do not cu ucher-resoutio o 19. separations of peptides and metabolites and new databases for ase molecules molecular assignm ents.These technological and computational mproven nts w be vital o the decade 1114622012 the influe olex inte of microbial communities on ecosystem sustainability and health 23. of the Such in-depth knowledge of microbial 6-74(200 ommunity phenomes e a better und anding of w perturbations s ab d 25 improved ccoystem sustainability and human health strategics 26 ACKNOWL thank N.Jo and C.Brisla assista er Hon 8,146414752014 et ol onolpil5 earch (Ge inD 208-212 5NE1.9.101 1023(2015) 0. 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Several other challenges that need to be addressed for better microbiome analyses include: extraction of biomolecules from highly diverse and complex sample matrices, such as soil, sediments and the human gut; assembly of complete genomes rather than sequence fragments directly from complex ecosystems; higher speed, throughput and dynamic range of MS technologies for metaproteomic and metabolomic measurements; meeting the high computational RAM requirements for de novo assembly of large metagenomes and metatranscriptomes16; sufficient storage and analysis options for terabytes to petabytes of data; and developing statistical and mathematical models to integrate the data and provide meaningful biological insights. Challenges aside, the future looks very bright for microbiome research. Recently, the White House Office of Science and Technology Policy (OSTP) announced a National Microbiome Initiative with funding from several federal agencies, industries and foundations focusing on improved technologies for understanding microbiomes5,45. We believe this initiative will prompt even faster and more informative nucleic acid sequencing and MS analyses, in addition to the development of bioinformatics programs that can quickly analyze microbiomes from a variety of ecosystems. We also expect the initiative will enable new technologies that do not currently exist, such as higher-resolution ion-mobility separations of peptides and metabolites and new databases for molecular assignments. These technological and computational improvements will be vital over the next decade for deciphering the roles of microbes in their natural habitats and determining the influence of the complex interplay between members of microbial communities on ecosystem sustainability and health. Such in-depth knowledge of microbial community phenomes will facilitate a better understanding of how perturbations such as climate change and disease affect microbiome functions, enabling better predictions of the impacts of these changes and facilitating improved ecosystem sustainability and human health strategies. ACKNOWLEDGMENTS We thank N. Johnson and C. Brislawn for their assistance in preparing the figures. This research was supported by the Pan-omics Program that is funded by the US Department of Energy’s Office of Biological and Environmental Research (Genomic Science Program) and the Microbiomes in Transition (MinT) Laboratory Directed Research and Development Initiative at the Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is a multi-program national laboratory operated by Battelle for the Department of Energy under contract DE-AC06-76RL01830. AUTHOR CONTRIBUTIONS R.A.W., S.J.C., R.J.M., E.S.B. and J.K.J. all contributed to this work and commented on the manuscript at all stages. COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. Reprints and permissions information is available online at http://www.nature. com/reprints/index.html. 1. Locey, K.J. & Lennon, J.T. Scaling laws predict global microbial diversity. Proc. Natl. Acad. Sci. USA 113, 5970–5975 (2016). 2. Jansson, J.K. Towards “Tera-Terra”: Terabase sequencing of terrestrial metagenomes. eScholarship http://escholarship.org/uc/item/04p1x29k. 2011. 3. Lamendella, R., VerBerkmoes, N. & Jansson, J.K. ‘Omics’ of the mammalian gut—new insights into function. Curr. Opin. Biotechnol. 23, 491–500 (2012). 4. Gilbert, J.A., Jansson, J.K. & Knight, R. The Earth Microbiome project: successes and aspirations. BMC Biol. 12, 69 (2014). npg © 2016 Nature America, Inc. All rights reserved