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The past, present and future of microbiome analyses

Nature Protocols volume 11, pages 2049–2053 (2016)Cite this article

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Abstract

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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References

  1. Locey, K.J. & Lennon, J.T. Scaling laws predict global microbial diversity. Proc. Natl. Acad. Sci. USA 113, 5970–5975 (2016).

    Article  CAS  Google Scholar 

  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).

    Article  CAS  Google Scholar 

  4. Gilbert, J.A., Jansson, J.K. & Knight, R. The Earth Microbiome project: successes and aspirations. BMC Biol. 12, 69 (2014).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  6. Lozupone, C.A., Stombaugh, J.I., Gordon, J.I., Jansson, J.K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012).

    Article  CAS  Google Scholar 

  7. Heather, J.M. & Chain, B. The sequence of sequencers: The history of sequencing DNA. Genomics 107, 1–8 (2016).

    Article  CAS  Google Scholar 

  8. Sanger, F., Nicklen, S. & Coulson, A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463–5467 (1977).

    Article  CAS  Google Scholar 

  9. Fleischmann, R.D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 (1995).

    Article  CAS  Google Scholar 

  10. Blattner, F.R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1462 (1997).

    Article  CAS  Google Scholar 

  11. Loman, N.J. et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 30, 434–439 (2012).

    Article  CAS  Google Scholar 

  12. Ronaghi, M., Uhlén, M. & Nyrén, P. A sequencing method based on real-time pyrophosphate. Science 281, 363, 365 (1998).

    Article  Google Scholar 

  13. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).

    Article  CAS  Google Scholar 

  14. Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008).

    Article  CAS  Google Scholar 

  15. Voskoboynik, A. et al. The genome sequence of the colonial chordate, Botryllus schlosseri. eLife 2, e00569 (2013).

    Article  Google Scholar 

  16. White, R.A. III et al. Moleculo long-read sequencing facilitates assembly and genomic binning from complex soil metagenomes. mSystems 1, e00045–16 (2016).

    Article  Google Scholar 

  17. Sharon, I. et al. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res. 25, 534–543 (2015).

    Article  CAS  Google Scholar 

  18. Kuleshov, V. et al. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat. Biotechnol. 34, 64–69 (2016).

    Article  CAS  Google Scholar 

  19. Levene, M.J. et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682–686 (2003).

    Article  CAS  Google Scholar 

  20. Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009).

    Article  CAS  Google Scholar 

  21. Murray, I.A. et al. The methylomes of six bacteria. Nucleic Acids Res. 40, 11450–11462 (2012).

    Article  CAS  Google Scholar 

  22. Laver, T. et al. Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol. Detect. Quantif. 3, 1–8 (2015).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  24. Willing, B.P. et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844–1854 e1 (2010).

    Article  Google Scholar 

  25. Mason, O.U. et al. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J. 6, 1715–1727 (2012).

    Article  CAS  Google Scholar 

  26. Mason, O.U. et al. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J. 8, 1464–1475 (2014).

    Article  CAS  Google Scholar 

  27. Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368–371 (2011).

    Article  CAS  Google Scholar 

  28. Hultman, J. et al. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521, 208–212 (2015).

    Article  CAS  Google Scholar 

  29. Goltsman, D.S.A., Comolli, L.R., Thomas, B.C. & Banfield, J.F. Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME J. 9, 1014–1023 (2015).

    Article  Google Scholar 

  30. Zoetendal, E.G. et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 6, 1415–1426 (2012).

    Article  CAS  Google Scholar 

  31. Shi, Y., Tyson, G.W., Eppley, J.M. & DeLong, E.F. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J. 5, 999–1013 (2011).

    Article  CAS  Google Scholar 

  32. Frias-Lopez, J. et al. Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. USA 105, 3805–3810 (2008).

    Article  CAS  Google Scholar 

  33. Shi, Y., Tyson, G.W. & DeLong, E.F. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459, 266–269 (2009).

    Article  CAS  Google Scholar 

  34. Gilbert, J.A. et al. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3, e3042 (2008).

    Article  Google Scholar 

  35. Gilbert, J.A. et al. Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Stand. Genomic Sci. 3, 183–193 (2010).

    Article  Google Scholar 

  36. Yamashita, M. & Fenn, J.B. Negative ion source production with electrospray ion source. J. Phys. Chem. 88, 4671–4675 (1984).

    Article  CAS  Google Scholar 

  37. Hu, Q., Noll, R.J., Li, H., Makarov, A., Hardman, M. & Graham Cooks, R. The Orbitrap: a new mass spectrometer. J. Mass Spectrom. 40, 430–443 (2005).

    Article  CAS  Google Scholar 

  38. Kelly, R.T., Tolmachev, A.V., Page, J.S., Tang, K. & Smith, R.D. The ion funnel: theory, implementations, and applications. Mass Spectrom. Rev. 29, 294–312 (2010).

    PubMed  PubMed Central  Google Scholar 

  39. Baker, E.S. et al. Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry. Mol. Cell. Proteomics 13, 1119–1127 (2014).

    Article  CAS  Google Scholar 

  40. Baker, E.S. et al. Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics 15, 2766–2776 (2015).

    Article  CAS  Google Scholar 

  41. Ram, R.J. et al. Community proteomics of a natural microbial biofilm. Science 308, 1915–1920 (2005).

    Article  CAS  Google Scholar 

  42. Aylward, F.O. et al. Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl. Environ. Microbiol. 79, 3770–3778 (2013).

    Article  CAS  Google Scholar 

  43. Aylward, F.O. et al. Enrichment and broad representation of plant biomass-degrading enzymes in the specialized hyphal swellings of Leucoagaricus gongylophorus, the fungal symbiont of leaf-cutter ants. PLoS One 10, e0134752 (2015).

    Article  Google Scholar 

  44. Huang, E.L. et al. The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environ. Microbiol. Rep. 6, 389–395 (2014).

    Article  Google Scholar 

  45. Burnum, K.E. et al. Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J. 5, 161–164 (2011).

    Article  CAS  Google Scholar 

  46. Verberkmoes, N.C. et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 3, 179–189 (2009).

    Article  CAS  Google Scholar 

  47. Handley, K.M. et al. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J. 7, 800–816 (2013).

    Article  CAS  Google Scholar 

  48. Wilmes, P., Heintz-Bus,. & Bond, P.L. A decade of metaproteomics: where we stand and what the future holds. Proteomics 15, 3409–3417 (2015).

    Article  CAS  Google Scholar 

  49. Jansson, J.K. & Baker, E.S. A multi-omic future for microbiome studies. Nat. Microbiol. 1, 16049 (2016).

    Article  CAS  Google Scholar 

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Acknowledgements

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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  1. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA

    Richard Allen White III, Stephen J Callister, Ronald J Moore, Erin S Baker & Janet K Jansson

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  1. Richard Allen White III
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  2. Stephen J Callister
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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.

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Correspondence to Erin S Baker or Janet K Jansson.

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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). https://doi.org/10.1038/nprot.2016.148

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