Advertisement

Genomes and Post-genome Technology

Reference work entry
  • 4.4k Downloads

Abstract

The beginning of the twenty-first century marks the genomic era in microbiology, where many genomes started being completely sequenced. The rate at which this kind of feat is now possible has increased drastically with the development of new sequencing technologies. In this post-genomic scenario, intraspecies genome variation has been examined and the concept of pan-genome, the sum of all genes present in members of one taxonomic group, was proposed. Practical application of this concept is found in the search for universal antigens for vaccine development. On a more fundamental level, these genome comparisons have increased the debate on what is a bacterial species and have shown that lateral gene transfer is more important than previously thought in bacterial genome evolution. Sequencing of the genomes from entire microbial communities has shown that the diversity of microorganisms is much greater than previously thought. Available post-genome technology has allowed the development of successful commercial biotechnology products without resorting to the cultivation of the microorganism of interest. On the opposite side of the spectrum, single cell genomics has allowed sequencing of the genome from individual cells. Accessing these genomes will give a perspective of genome differences between individuals and will facilitate the cultivation of these organisms. Central to all these developments in genome and post-genome technologies is bioinformatics. Some of the strategies used for genome and metagenome data storage and analysis are discussed. Although there are a number of successful examples, the challenge now is to transform the knowledge about genomes and post-genome technologies into commercial products at a greater pace.

Keywords

Microbial Community Cloud Computing Anaerobic Ammonium Oxidation Core Genome Metagenomic Library 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We thank Samuel Dias Araújo Júnior for making figures and Dr. David Weiner for providing information about commercial enzyme products, and also CAPES, FAP-DF, and CNPq for funding.

References

  1. Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF (2011) CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics 12:356PubMedGoogle Scholar
  2. Ansorge WJ (2009) Next-generation DNA sequencing techniques. N Biotechnol 25:195–203PubMedGoogle Scholar
  3. Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P (2010) SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics 26:2977–2978PubMedGoogle Scholar
  4. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Antolin M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Merieux A, Melo Minardi R, M’Rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P (2011) Enterotypes of the human gut microbiome. Nature 473:174–180PubMedGoogle Scholar
  5. Baker-Austin C, Dopson M (2007) Life in acid: pH homeostasis in acidophiles. Trends Microbiol 15:165–171PubMedGoogle Scholar
  6. Baldrian P, Kolarik M, Stursova M, Kopecky J, Valaskova V, Vetrovsky T, Zifcakova L, Snajdr J, Ridl J, Vlcek C, Voriskova J (2011) Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J 6:248–258PubMedGoogle Scholar
  7. Beloqui A, Pita M, Polaina J, Martinez-Arias A, Golyshina OV, Zumarraga M, Yakimov MM, Garcia-Arellano H, Alcalde M, Fernandez VM, Elborough K, Andreu JM, Ballesteros A, Plou FJ, Timmis KN, Ferrer M, Golyshin PN (2006) Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis, and phylogenetic relationships. J Biol Chem 281:22933–22942PubMedGoogle Scholar
  8. Beloqui A, Nechitaylo TY, Lopez-Cortes N, Ghazi A, Guazzaroni ME, Polaina J, Strittmatter AW, Reva O, Waliczek A, Yakimov MM, Golyshina OV, Ferrer M, Golyshin PN (2010) Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species. Appl Environ Microbiol 76:5934–5946PubMedGoogle Scholar
  9. Benders GA, Noskov VN, Denisova EA, Lartigue C, Gibson DG, Assad-Garcia N, Chuang RY, Carrera W, Moodie M, Algire MA, Phan Q, Alperovich N, Vashee S, Merryman C, Venter JC, Smith HO, Glass JI, Hutchison CA 3rd (2010) Cloning whole bacterial genomes in yeast. Nucleic Acids Res 38:2558–2569PubMedGoogle Scholar
  10. Several Authors (2008) Big data. Nature 455:1. Nature special issueGoogle Scholar
  11. Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS One 6:e16626PubMedGoogle Scholar
  12. Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D (2006) The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7:169PubMedGoogle Scholar
  13. Bomar L, Maltz M, Colston S, Graf J (2011) Directed culturing of microorganisms using metatranscriptomics. MBio 2(2):e00012-11PubMedGoogle Scholar
  14. Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol 14:274PubMedGoogle Scholar
  15. Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 106:1948–1953PubMedGoogle Scholar
  16. Button DK, Schut F, Quang P, Martin R, Robertson BR (1993) Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl Environ Microbiol 59:881–891PubMedGoogle Scholar
  17. Chistoserdova L (2010) Recent progress and new challenges in metagenomics for biotechnology. Biotechnol Lett 32:1351–1359PubMedGoogle Scholar
  18. Chistoserdovai L (2010) Functional metagenomics: recent advances and future challenges. Biotechnol Genet Eng Rev 26:335–352PubMedGoogle Scholar
  19. Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo M-J, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS (2011) De Novo assembly of bacterial genomes from single cells. Nat Biotechnol 29:915PubMedGoogle Scholar
  20. Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878–3885PubMedGoogle Scholar
  21. Cuadros-Orellana S, Martin-Cuadrado AB, Legault B, D’Auria G, Zhaxybayeva O, Papke RT, Rodriguez-Valera F (2007) Genomic plasticity in prokaryotes: the case of the square haloarchaeon. ISME J 1:235–245PubMedGoogle Scholar
  22. de Castro AP, Quirino BF, Allen H, Williamson LL, Handelsman J, Kruger RH (2011) Construction and validation of two metagenomic DNA libraries from Cerrado soil with high clay content. Biotechnol Lett 33:2169PubMedGoogle Scholar
  23. de Jager V, Siezen RJ (2011) Single-cell genomics: unravelling the genomes of unculturable microorganisms. Microb Biotechnol 4:431–437PubMedGoogle Scholar
  24. Dean FB, Nelson JR, Giesler TL, Lasken RS (2001) Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11:1095–1099PubMedGoogle Scholar
  25. Deloger M, El Karoui M, Petit MA (2009) A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol 191:91–99PubMedGoogle Scholar
  26. Doolittle WF, Papke RT (2006) Genomics and the bacterial species problem. Genome Biol 7:116PubMedGoogle Scholar
  27. Dumon C, Varvak A, Wall MA, Flint JE, Lewis RJ, Lakey JH, Morland C, Luginbuhl P, Healey S, Todaro T, DeSantis G, Sun M, Parra-Gessert L, Tan X, Weiner DP, Gilbert HJ (2008) Engineering hyperthermostability into a GH11 xylanase is mediated by subtle changes to protein structure. J Biol Chem 283:22557–22564PubMedGoogle Scholar
  28. Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D (2011) Haloquadratum walsbyi: limited diversity in a global pond. PLoS One 6:e20968PubMedGoogle Scholar
  29. Ehrlich GD, Ahmed A, Earl J, Hiller NL, Costerton JW, Stoodley P, Post JC, DeMeo P, Hu FZ (2010) The distributed genome hypothesis as a rubric for understanding evolution in situ during chronic bacterial biofilm infectious processes. FEMS Immunol Med Microbiol 59:269–279PubMedGoogle Scholar
  30. Fernandez-Arrojo L, Guazzaroni ME, Lopez-Cortes N, Beloqui A, Ferrer M (2010) Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 21:725–733PubMedGoogle Scholar
  31. Ferrari BC, Oregaard G, Sorensen SJ (2004) Recovery of GFP-labeled bacteria for culturing and molecular analysis after cell sorting using a benchtop flow cytometer. Microb Ecol 48:239–245PubMedGoogle Scholar
  32. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512PubMedGoogle Scholar
  33. Frohlich J, Konig H (1999) Rapid isolation of single microbial cells from mixed natural and laboratory populations with the aid of a micromanipulator. Syst Appl Microbiol 22:249–257PubMedGoogle Scholar
  34. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, Smith HO (2008a) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319:1215–1220PubMedGoogle Scholar
  35. Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA 3rd (2008b) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci USA 105:20404–20409PubMedGoogle Scholar
  36. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52–56PubMedGoogle Scholar
  37. Glass JI, Hutchison CA 3rd, Smith HO, Venter JC (2009) A systems biology tour de force for a near-minimal bacterium. Mol Syst Biol 5:330PubMedGoogle Scholar
  38. Gomez-Alvarez V, Teal TK, Schmidt TM (2009) Systematic artifacts in metagenomes from complex microbial communities. ISME J 3:1314–1317PubMedGoogle Scholar
  39. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91PubMedGoogle Scholar
  40. Hall BG, Ehrlich GD, Hu FZ (2010) Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing. Microbiology 156:1060–1068PubMedGoogle Scholar
  41. Han S, Lee J, Kim W, Shin HJ, Kim G (2008) Screening of promoters from metagenomic DNA and their use for the construction of expression vectors. J Microbiol Biotechnol 18:1634–1640PubMedGoogle Scholar
  42. Harrison PM, Arosio P (1996) The ferritins: molecular properties, iron storage function and cellular regulation. Biochim Biophys Acta 1275:161–203PubMedGoogle Scholar
  43. Heywood JL, Sieracki ME, Bellows W, Poulton NJ, Stepanauskas R (2011) Capturing diversity of marine heterotrophic protists: one cell at a time. ISME J 5:674–684PubMedGoogle Scholar
  44. Hogg JS, Hu FZ, Janto B, Boissy R, Hayes J, Keefe R, Post JC, Ehrlich GD (2007) Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol 8:R103PubMedGoogle Scholar
  45. Horner DS, Pavesi G, Castrignano T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G (2009) Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform 11:181–197PubMedGoogle Scholar
  46. Ishoy T, Kvist T, Westermann P, Ahring BK (2006) An improved method for single cell isolation of prokaryotes from meso-, thermo- and hyperthermophilic environments using micromanipulation. Appl Microbiol Biotechnol 69:510–514PubMedGoogle Scholar
  47. Kang Y, Norris MH, Zarzycki-Siek J, Nierman WC, Donachie SP, Hoang TT (2011) Transcript amplification from single bacterium for transcriptome analysis. Genome Res 21:925–935PubMedGoogle Scholar
  48. Kim EY, Oh KH, Lee MH, Kang CH, Oh TK, Yoon JH (2009) Novel cold-adapted alkaline lipase from an intertidal flat metagenome and proposal for a new family of bacterial lipases. Appl Environ Microbiol 75:257–260PubMedGoogle Scholar
  49. Kislyuk AO, Haegeman B, Bergman NH, Weitz JS (2011) Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genomics 12:32PubMedGoogle Scholar
  50. Klenk HP, Göker M (2010) En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 33:175–182PubMedGoogle Scholar
  51. Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572PubMedGoogle Scholar
  52. Konstantinidis KT, Ramette A, Tiedje JM (2006) The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361:1929–1940PubMedGoogle Scholar
  53. Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A (2009) Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Res 19:2144–2153PubMedGoogle Scholar
  54. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2009) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118–123PubMedGoogle Scholar
  55. Lagesen K, Ussery DW, Wassenaar TM (2010) Genome update: the 1000th genome–a cautionary tale. Microbiology 156:603–608PubMedGoogle Scholar
  56. Lan R, Reeves PR (2001) When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol 9:419–424PubMedGoogle Scholar
  57. Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome. Trends Genet 25:107–110PubMedGoogle Scholar
  58. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC (2007) Genome transplantation in bacteria: changing one species to another. Science 317:632–638PubMedGoogle Scholar
  59. Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, Noskov VN, Denisova EA, Gibson DG, Assad-Garcia N, Alperovich N, Thomas DW, Merryman C, Hutchison CA 3rd, Smith HO, Venter JC, Glass JI (2009) Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325:1693–1696PubMedGoogle Scholar
  60. Lefébure T, Stanhope MJ (2007) Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8:R71PubMedGoogle Scholar
  61. Legault BA, Lopez-Lopez A, Alba-Casado JC, Doolittle WF, Bolhuis H, Rodriguez-Valera F, Papke RT (2006) Environmental genomics of “Haloquadratum walsbyi” in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics 7:171PubMedGoogle Scholar
  62. Liu N, Yan X, Zhang M, Xie L, Wang Q, Huang Y, Zhou X, Wang S, Zhou Z (2011) Microbiome of fungus-growing termites: a new reservoir for lignocellulase genes. Appl Environ Microbiol 77:48–56PubMedGoogle Scholar
  63. Lopez-Garcia P, Moreira D (2008) Tracking microbial biodiversity through molecular and genomic ecology. Res Microbiol 159:67–73PubMedGoogle Scholar
  64. Lu Y, Yu Y, Zhou R, Sun W, Dai C, Wan P, Zhang L, Hao D, Ren H (2011) Cloning and characterisation of a novel 2,4-dichlorophenol hydroxylase from a metagenomic library derived from polychlorinated biphenyl-contaminated soil. Biotechnol Lett 33:1159–1167PubMedGoogle Scholar
  65. Lukjancenko O, Wassenaar TM, Ussery DW (2010) Comparison of 61 Sequenced Escherichia coli Genomes. Microb Ecol 60:708–720PubMedGoogle Scholar
  66. MacLean D, Jones JD, Studholme DJ (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev Microbiol 7:287–296PubMedGoogle Scholar
  67. Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, Tettelin H, Brettoni C, Iacobini ET, Rosini R, D’Agostino N, Miorin L, Buccato S, Mariani M, Galli G, Nogarotto R, Nardi Dei V, Vegni F, Fraser C, Mancuso G, Teti G, Madoff LC, Paoletti LC, Rappuoli R, Kasper DL, Telford JL, Grandi G (2005) Identification of a universal Group B Streptococcus vaccine by multiple genome screen. Science 309:148–150PubMedGoogle Scholar
  68. Majernik A, Gottschalk G, Daniel R (2001) Screening of environmental DNA libraries for the presence of genes conferring Na(+)(Li(+))/H(+) antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. J Bacteriol 183:6645–6653PubMedGoogle Scholar
  69. Marcy Y, Ouverney C, Bik EM, Losekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR (2007) Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104:11889–11894PubMedGoogle Scholar
  70. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15:589–594PubMedGoogle Scholar
  71. Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, Falkow S, Rappuoli R (2008) Microbiology in the post-genomic era. Nat Rev Microbiol 6:419–430PubMedGoogle Scholar
  72. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386PubMedGoogle Scholar
  73. Mira A, Martin-Cuadrado AB, D’Auria G, Rodriguez-Valera F (2010) The bacterial pan-genome:a new paradigm in microbiology. Int Microbiol 13:45–57PubMedGoogle Scholar
  74. Morgan JL, Darling AE, Eisen JA (2010) Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One 5:e10209PubMedGoogle Scholar
  75. Mussmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jorgensen BB, Huntemann M, Glockner FO, Amann R, Koopman WJ, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD (2007) Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 5:e230PubMedGoogle Scholar
  76. Muzzi A, Masignani V, Rappuoli R (2007) The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. Drug Discov Today 12:429–439PubMedGoogle Scholar
  77. Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methe BA, Palsson BO, Lovley DR, Barrett CL (2010) De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. PLoS One 5:e10922PubMedGoogle Scholar
  78. Newman DJ, Cragg GM (2005) The discovery of anticancer drugs from natural sources. In: Zhang L, Demain AL (eds) Natural products: drug discovery and therapeutic medicine. Humana Press, Totowan, pp 128–168Google Scholar
  79. Oh D, Porter K, Russ B, Burns D, Dyall-Smith M (2010) Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds. Extremophiles 14:161–169PubMedGoogle Scholar
  80. Ottesen EA, Hong JW, Quake SR, Leadbetter JR (2006) Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314:1464–1467PubMedGoogle Scholar
  81. Pang H, Zhang P, Duan CJ, Mo XC, Tang JL, Feng JX (2009) Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase. Curr Microbiol 58:404–408PubMedGoogle Scholar
  82. Parachin NS, Gorwa-Grauslund MF (2011) Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenome library. Biotechnol Biofuels 4:9PubMedGoogle Scholar
  83. Park SY, Shin HJ, Kim GJ (2011) Screening and identification of a novel esterase EstPE from a metagenomic DNA library. J Microbiol 49:7–14PubMedGoogle Scholar
  84. Pathak GP, Ehrenreich A, Losi A, Streit WR, Gartner W (2009) Novel blue light-sensitive proteins from a metagenomic approach. Environ Microbiol 11:2388–2399PubMedGoogle Scholar
  85. Podar M, Abulencia CB, Walcher M, Hutchison D, Zengler K, Garcia JA, Holland T, Cotton D, Hauser L, Keller M (2007) Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol 73:3205–3214PubMedGoogle Scholar
  86. Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, McHardy AC, Cheng JF, Hugenholtz P, McSweeney CS, Morrison M (2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci USA 107:14793–14798PubMedGoogle Scholar
  87. Porter J, Edwards C, Morgan JA, Pickup RW (1993) Rapid, automated separation of specific bacteria from lake water and sewage by flow cytometry and cell sorting. Appl Environ Microbiol 59:3327–3333PubMedGoogle Scholar
  88. Portnoy VA, Bezdan D, Zengler K (2011) Adaptive laboratory evolution-harnessing the power of biology for metabolic engineering. Curr Opin Biotechnol 22:590–594PubMedGoogle Scholar
  89. Purdy KJ (2005) Nucleic acid recovery from complex environmental samples. Methods Enzymol 397:271–292PubMedGoogle Scholar
  90. Raghunathan A, Ferguson HR Jr, Bornarth CJ, Song W, Driscoll M, Lasken RS (2005) Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71:3342–3347PubMedGoogle Scholar
  91. Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J (2008) The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–6893PubMedGoogle Scholar
  92. Rhee JK, Ahn DG, Kim YG, Oh JW (2005) New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl Environ Microbiol 71:817–825PubMedGoogle Scholar
  93. Richardson TH, Tan X, Frey G, Callen W, Cabell M, Lam D, Macomber J, Short JM, Robertson DE, Miller C (2002) A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase. J Biol Chem 277:26501–26507PubMedGoogle Scholar
  94. Riesenfeld CS, Goodman RM, Handelsman J (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6:981–989PubMedGoogle Scholar
  95. Robertson DE, Chaplin JA, DeSantis G, Podar M, Madden M, Chi E, Richardson T, Milan A, Miller M, Weiner DP, Wong K, McQuaid J, Farwell B, Preston LA, Tan X, Snead MA, Keller M, Mathur E, Kretz PL, Burk MJ, Short JM (2004) Exploring nitrilase sequence space for enantioselective catalysis. Appl Environ Microbiol 70:2429–2436PubMedGoogle Scholar
  96. Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW (2009) Whole genome amplification and de novo assembly of single bacterial cells. PLoS One 4:e6864PubMedGoogle Scholar
  97. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547PubMedGoogle Scholar
  98. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP (2010) Computational solutions to large-scale data management and analysis. Nat Rev Genet 11:647–657PubMedGoogle Scholar
  99. Schallmey M, Ly A, Wang C, Meglei G, Voget S, Streit WR, Driscoll BT, Charles TC (2011) Harvesting of novel polyhydroxyalkanaote (PHA) synthase encoding genes from a soil metagenome library using phenotypic screening. FEMS Microbiol Lett 321:150–156PubMedGoogle Scholar
  100. Schwartz S, Oren R, Ast G (2011) Detection and removal of biases in the analysis of next-generation sequencing reads. PLoS One 6:e16685PubMedGoogle Scholar
  101. Sharp KH, Davidson SK, Haygood MG (2007) Localization of ‘Candidatus Endobugula sertula’ and the bryostatins throughout the life cycle of the bryozoan Bugula neritina. ISME J 1:693–702PubMedGoogle Scholar
  102. Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U (2010) Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 5:61–70PubMedGoogle Scholar
  103. Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77:1153–1161PubMedGoogle Scholar
  104. Simon C, Herath J, Rockstroh S, Daniel R (2009) Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice. Appl Environ Microbiol 75:2964–2968PubMedGoogle Scholar
  105. Sogin ML, Morrison HG, Huber JA, Mark Welch D, 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 103:12115–12120PubMedGoogle Scholar
  106. Stepanauskas R, Sieracki ME (2007) Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci USA 104:9052–9057PubMedGoogle Scholar
  107. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Medigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M, Le Paslier D (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790–794PubMedGoogle Scholar
  108. Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomas AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR (2010) An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet 6:e1001129PubMedGoogle Scholar
  109. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J (2011) Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res 39:D546–D551PubMedGoogle Scholar
  110. Suzuki S, Ono N, Furusawa C, Ying BW, Yomo T (2011) Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS One 6:e19534PubMedGoogle Scholar
  111. Tadmor AD, Ottesen EA, Leadbetter JR, Phillips R (2011) Probing individual environmental bacteria for viruses by using microfluidic digital PCR. Science 333:58–62PubMedGoogle Scholar
  112. Tanenbaum DM, Goll J, Murphy S, Kumar P, Zafar N, Thiagarajan M, Madupu R, Davidsen T, Kagan L, Kravitz S, Rusch DB, Yooseph S (2010) The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data. Stand Genomic Sci 2:229–237PubMedGoogle Scholar
  113. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6:377–382PubMedGoogle Scholar
  114. Taniguchi K, Kajiyama T, Kambara H (2009) Quantitative analysis of gene expression in a single cell by qPCR. Nat Methods 6:503–506PubMedGoogle Scholar
  115. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329:533–538PubMedGoogle Scholar
  116. Taupp M, Mewis K, Hallam SJ (2011) The art and design of functional metagenomic screens. Curr Opin Biotechnol 22:465–472PubMedGoogle Scholar
  117. Taylor RJ, Falconnet D, Niemisto A, Ramsey SA, Prinz S, Shmulevich I, Galitski T, Hansen CL (2009) Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform. Proc Natl Acad Sci USA 106:3758–3763PubMedGoogle Scholar
  118. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarity Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA 102:13950–13955PubMedGoogle Scholar
  119. Tettelin H, Riley D, Cattuto C, Medini D (2008) Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 11:472–477PubMedGoogle Scholar
  120. Tsuruta H, Paddon CJ, Eng D, Lenihan JR, Horning T, Anthony LC, Regentin R, Keasling JD, Renninger NS, Newman JD (2009) High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS One 4:e4489PubMedGoogle Scholar
  121. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43PubMedGoogle Scholar
  122. Uchiyama T, Abe T, Ikemura T, Watanabe K (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23:88–93PubMedGoogle Scholar
  123. Ussery DW, Kiil K, Lagesen K, Sicheritz-Ponten T, Bohlin J, Wassenaar TM (2009) The genus Burkholderia: analysis of 56 genomic sequences. Genome Dyn 6:140–157PubMedGoogle Scholar
  124. 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 304:66–74PubMedGoogle Scholar
  125. Walker A, Parkhill J (2008) Single-cell genomics. Nat Rev Microbiol 6:176–177PubMedGoogle Scholar
  126. Wang C, Meek DJ, Panchal P, Boruvka N, Archibald FS, Driscoll BT, Charles TC (2006) Isolation of poly-3-hydroxybutyrate metabolism genes from complex microbial communities by phenotypic complementation of bacterial mutants. Appl Environ Microbiol 72:384–391PubMedGoogle Scholar
  127. Wender PA, Miller BL (2009) Synthesis at the molecular frontier. Nature 460:197–201PubMedGoogle Scholar
  128. Wooley JC, Godzik A, Friedberg I (2010) A primer on metagenomics. PLoS Comput Biol 6:e1000667PubMedGoogle Scholar
  129. Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R (2009) Assembling the marine metagenome, one cell at a time. PLoS One 4:e5299PubMedGoogle Scholar
  130. Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF (2010) One bacterial cell, one complete genome. PLoS One 5:e10314PubMedGoogle Scholar
  131. Wu S, Zhu Z, Fu L, Niu B, Li W (2011) WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12:444PubMedGoogle Scholar
  132. Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D (2011) Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332:714–717PubMedGoogle Scholar
  133. Yu EY, Kwon MA, Lee M, Oh JY, Choi JE, Lee JY, Song BK, Hahm DH, Song JK (2011) Isolation and characterization of cold-active family VIII esterases from an arctic soil metagenome. Appl Microbiol Biotechnol 90:573–581PubMedGoogle Scholar
  134. Zeng Y, Novak R, Shuga J, Smith MT, Mathies RA (2010) High-performance single cell genetic analysis using microfluidic emulsion generator arrays. Anal Chem 82:3183–3190PubMedGoogle Scholar
  135. Zengler K (2009) Central role of the cell in microbial ecology. Microbiol Mol Biol Rev 73:712–729PubMedGoogle Scholar
  136. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM (2006) Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24:680–686PubMedGoogle Scholar
  137. Zhao S, Wang J, Bu D, Liu K, Zhu Y, Dong Z, Yu Z (2010) Novel glycoside hydrolases identified by screening a Chinese Holstein dairy cow rumen-derived metagenome library. Appl Environ Microbiol 76:6701–6705PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Genomic Sciences and Biotechnology ProgramUniversidade Católica de BrasíliaBrasíliaBrazil
  2. 2.Embrapa-AgrienergyBrasíliaBrazil
  3. 3.Embrapa-Genetic Resources and BiotechnologyBioinformatics LaboratoryBrasíliaBrazil
  4. 4.Department of BioengineeringUniversity of CaliforniaSan Diego, La JollaUSA
  5. 5.J. Craig Venter InstituteRockvilleUSA
  6. 6.Biology InstituteUnB Brasília UniversityBrasíliaBrazil

Personalised recommendations