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The past, present and future of microbiome analyses


Over the last decade, technical advances in nucleic acid sequencing and mass spectrometry have enabled faster and more informative metagenomic, metatranscriptomic, metaproteomic and metabolomic measurements. Here we review key improvements in multi-omic environmental and human microbiome analyses, and discuss developments required to address current measurement shortcomings.

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Figure 1: Advances in sequencing technologies over the last decade.
Figure 2: The evolution of ion-trap-based MS instruments.
Figure 3


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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.

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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.

Corresponding authors

Correspondence to Erin S Baker or Janet K Jansson.

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The authors declare no competing financial interests.

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White, R., Callister, S., Moore, R. et al. The past, present and future of microbiome analyses. Nat Protoc 11, 2049–2053 (2016).

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