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Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream

Nature Biotechnology volume 27, pages 627–632 (2009)Cite this article

As we approach the completed sequencing of 1,000 microbial genomes, the field of microbial genomics is poised at a crossroads. The future holds great promise for far-reaching advancements in microbiology as well as in diverse, related sciences. But realizing that potential will require meeting the challenges that have accompanied the rapid development of the underlying technology and the exponential growth of data. New technologies provide unprecedented opportunities but also call for conceptual shifts. Experience gained in the first decade of genomics can guide the improved approaches now needed for the selection of genome sequencing projects and their funding, for genome publication and annotation, as well as for data analysis and access. Equipped with these new tools and policies, microbiologists will have a unique opportunity for unprecedented exploration of our microbial planet.

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Figure 1: Phylogenetic distribution of sequencing projects.

References

  1. Roberts, R.J. Identifying protein function–a call for community action. PLoS Biol. 2, E42 (2004).

    Article  Google Scholar 

  2. Woese, C.R. A manifesto for microbial genomics. Curr. Biol. 8, R781–R783 (1998).

    Article  CAS  Google Scholar 

  3. Liolios, K., Mavromatis, K., Tavernarakis, N. & Kyrpides, N.C. The Genomes OnLine Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 36, D475–D479 (2008).

    Article  CAS  Google Scholar 

  4. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Sayers, E.W. Genbank. Nucleic Acids Res. 37, D26–D31 (2009).

    Article  CAS  Google Scholar 

  5. Woese, C.R. A new biology for a new century. Microbiol. Mol. Biol. Rev. 68, 173–186 (2004).

    Article  CAS  Google Scholar 

  6. Stanhope, M.J. et al. Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 411, 940–944 (2001).

    Article  CAS  Google Scholar 

  7. DeLong, E.F. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3, 459–469 (2005).

    Article  CAS  Google Scholar 

  8. Kyrpides, N.C. & Ouzounis, C.A. Whole-genome sequence annotation: 'Going wrong with confidence'. Mol. Microbiol. 32, 886–887 (1999).

    Article  CAS  Google Scholar 

  9. Markowitz, V.M. Microbial genome data sources. Curr. Opin. Biotechnol. 18, 267–272 (2007).

    Article  CAS  Google Scholar 

  10. Garrity, G.M. et al. A new model of open access publishing: an ejournal for the Genomic Standards Consortium. OMICS 2, 157–60 (2008).

    Article  Google Scholar 

  11. Fox, G.E. et al. The phylogeny of prokaryotes. Science 209, 457–463 (1980).

    Article  CAS  Google Scholar 

  12. Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3, REVIEWS0003 (2002).

  13. Hugenholtz, P. & Kyrpides, N.C. A changing of the guard. Environ. Microbiol. 11, 551–553 (2009).

    Article  Google Scholar 

  14. Galperin, M.Y. & Cochrane, G.R. Nucleic Acids Research annual database issue and the NAR online Molecular Biology Database Collection in 2009. Nucleic Acids Res. 37, D1–D4 (2009).

    Article  CAS  Google Scholar 

  15. Huss, J.W. III, et al. A gene wiki for community annotation of gene function. PLoS Biol. 6, e175 (2008).

    Article  Google Scholar 

  16. Mons, B. et al. Calling on a million minds for community annotation in WikiProteins. Genome Biol. 9, R89 (2007).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  18. Markowitz, V.M. et al. The Integrated Microbial Genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 36, D528–D533 (2008).

    Article  CAS  Google Scholar 

  19. Nierman, W.C. et al. Structural flexibility in the Burkholderia mallei genome. Proc. Natl. Acad. Sci. USA 101, 14246–14251 (2004).

    Article  CAS  Google Scholar 

  20. Holden, M.T. et al. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc. Natl. Acad. Sci. USA 101, 14240–14245 (2004).

    Article  CAS  Google Scholar 

  21. Field, D. et al. The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol. 26, 541–547 (2008).

    Article  CAS  Google Scholar 

  22. Parkhill, J. Time to remove the model organism blinkers. Trends Microbiol. 16, 510–511 (2008).

    Article  CAS  Google Scholar 

  23. Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J. & Goodman, R.M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5, 245–249 (1998).

    Article  Google Scholar 

  24. Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. & Hugenholtz, P. A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev. 72, 557–578 (2008).

    Article  CAS  Google Scholar 

  25. Handelsman, J. et al. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet (The National Academies Press, Washington, DC, 2007).

    Google Scholar 

  26. Woese, C. The quest for Darwin's grail. ASM News 65, 260–263 (1999).

    Google Scholar 

  27. Altschul, S., Gish, W., Miller, W., Myers, E. & Lipman, D. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  Google Scholar 

  28. Oehmen, C.S. & Nieplocha, J. ScalaBLAST: A scalable implementation of BLAST for high performance data-intensive bioinformatics analysis. IEEE Trans. Parallel Dist. Sys. 17, 740–749 (2006).

    Article  Google Scholar 

  29. Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.” Proc. Natl. Acad. Sci. USA 102, 13950–13955 (2005).

    Article  CAS  Google Scholar 

  30. Kettler, G.C. et al. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet. 3, e231 (2007).

    Article  Google Scholar 

  31. Ishoey, T., Woyke, T., Stepanauskas, R., Novotny, M. & Lasken, R.S. Genomic sequencing of single microbial cells from environmental samples. Curr. Opin. Microbiol. 11, 198–204 (2008).

    Article  CAS  Google Scholar 

  32. Armengaud, J. A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr Opin Microbiol. 12, 292–300 (2009).

    Article  CAS  Google Scholar 

  33. Toledo-Arana, A. et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature 459, 950–956 (2009).

    Article  CAS  Google Scholar 

  34. Yooseph, S. et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 5, e16 (2007).

    Article  Google Scholar 

  35. Whitman, W.B., Coleman, D.C. & Wiebe, W.J. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95, 6578–6583 (1998).

    Article  CAS  Google Scholar 

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Acknowledgements

I would like to thank C. Woese, P. Hugenholtz and C. Ouzounis for their critical reading and helpful suggestions, and M. Youle for her excellent editorial assistance. Special thanks to the members of the Genome Biology Program at the Joint Genome Institute for keeping me constantly in a most challenging and stimulating environment.

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  1. Genome Biology Program, DOE Joint Genome Institute, Walnut Creek, California, USA

    Nikos C Kyrpides

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  1. Nikos C Kyrpides
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Correspondence to Nikos C Kyrpides.

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Kyrpides, N. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat Biotechnol 27, 627–632 (2009). https://doi.org/10.1038/nbt.1552

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