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Next-Generation Sequencing—the Promise and Perils of Charting the Great Microbial Unknown

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References

  1. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    PubMed  CAS  Google Scholar 

  2. Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173:4371–4378

    PubMed  CAS  Google Scholar 

  3. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    Article  PubMed  CAS  Google Scholar 

  4. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638

    Article  PubMed  Google Scholar 

  5. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359

    Article  PubMed  CAS  Google Scholar 

  6. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449:804–810

    Article  PubMed  CAS  Google Scholar 

  7. Anon (2008, posting date). National Institutes of Health Human Microbiome Project http://nihroadmap.nih.gov/hmp/. [Online.]

  8. Mullard A (2008) Microbiology: the inside story. Nature 453:578–580

    Article  PubMed  CAS  Google Scholar 

  9. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031

    Article  PubMed  Google Scholar 

  10. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI (2008) Evolution of mammals and their gut microbes. Science 320:1647–1651

    Article  PubMed  CAS  Google Scholar 

  11. Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC Jr, Rohwer F (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57

    Article  PubMed  Google Scholar 

  12. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA 103:12115–12120

    Article  PubMed  CAS  Google Scholar 

  13. Huber JA, Welch DBM, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100

    Article  PubMed  CAS  Google Scholar 

  14. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809

    Article  PubMed  CAS  Google Scholar 

  15. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, vanEngelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318:283–287

    Article  PubMed  CAS  Google Scholar 

  16. Doctorow C (2008) Big data: welcome to the petacentre. Nature 455:16–21

    Article  PubMed  CAS  Google Scholar 

  17. Waldrop M (2008) Big data: Wikiomics. Nature 455:22–25

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Centre for Systems Biology, University of Birmingham, Edgbaston, B15 2TT, UK

    Lori A. S. Snyder, Nick Loman & Mark J. Pallen

  2. School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK

    Charles W. Penn

Authors
  1. Lori A. S. Snyder
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  2. Nick Loman
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  3. Mark J. Pallen
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  4. Charles W. Penn
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Correspondence to Nick Loman.

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Snyder, L.A.S., Loman, N., Pallen, M.J. et al. Next-Generation Sequencing—the Promise and Perils of Charting the Great Microbial Unknown. Microb Ecol 57, 1–3 (2009). https://doi.org/10.1007/s00248-008-9465-9

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  • DOI: https://doi.org/10.1007/s00248-008-9465-9

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