Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Genome Atlases, Potential Applications in Study of Metagenomes

Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_686-1

Traditional microbiology has used a single species approach, as in Koch’s postulates, where a bacterium is shown to be pathogenic by first isolation from infected organisms, then grown in monoculture, and finally reintroduced into healthy individuals and causing the disease. In contrast, microbial ecology studies multispecies and community structures. Both of these areas have been very successful, and these two different approaches can be seen in comparative genomics, with the traditional analysis of single genomes versus many genomes or metagenomes isolated from an environment. It is possible to relate microbial ecology to reductionist, monoculture microbiology by comparing the two different data types. In this case, the reference is the single genome of an organism, the other being the metagenome samples where most of the DNA in the environment is sampled. Surely, the comparisons are most reliable when the environmental DNA is preferably in chunks containing at least several genes –...

Keywords

Acid Mine Drainage Amino Sugar Metagenome Sample Marine Microbe Global Ocean Sampling 
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.
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References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.PubMedCrossRefGoogle Scholar
  2. Baldi P, Brunak S, Chauvin Y, Krogh A. Naturally occurring nucleosome positioning signals in human exons and introns. J Mol Biol. 1996;263(4):503–10.PubMedCrossRefGoogle Scholar
  3. Bolshoy A, McNamara P, Harrington RE, Trifonov EN. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci USA. 1991;88:2312–6.PubMedCentralPubMedCrossRefGoogle Scholar
  4. Brown MV, Lauro FM, DeMaere MZ, et al. Global biogeography of SAR11 marine bacteria. Mol Syst Biol. 2012;8:595.PubMedCentralPubMedCrossRefGoogle Scholar
  5. DeLong EF, Preston CM, Mincer T, et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 2006;311(5760):496–503.PubMedCrossRefGoogle Scholar
  6. García-Martínez J, Rodríguez-Valera F. Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of group I. Mol Ecol. 2000;9(7):935–48.PubMedCrossRefGoogle Scholar
  7. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990;345(6270):60–3.PubMedCrossRefGoogle Scholar
  8. Giovannoni SJ, Tripp HJ, Givan S, et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science. 2005;309(5738):1242–5.PubMedCrossRefGoogle Scholar
  9. Hallin PF, Binnewies TT, Ussery DW. The genome BLAST atlas – a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst. 2008;4(5):363–71.PubMedCrossRefGoogle Scholar
  10. Huo Y-Y, Cheng H, Han X-F, et al. Complete genome sequence of Pelagibacterium halotolerans B2(T). J Bacteriol. 2012;194(1):197–8.PubMedCentralPubMedCrossRefGoogle Scholar
  11. Jensen LJ, Friis C, Ussery DW. Three views of microbial genomes. Res Microbiol. 1999;150(9–10):773–7.PubMedCrossRefGoogle Scholar
  12. Kalyuzhnaya MG, Lapidus A, Ivanova N, et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. 2008;26(9):1029–34.PubMedCrossRefGoogle Scholar
  13. Markowitz VM, Chen I-MA, Chu K, et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 2012;40(Database issue):D123–9.PubMedCentralPubMedCrossRefGoogle Scholar
  14. Ornstein RL, Rein R, Breen DL, MacElroy R. An optimised potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers. 1978;17:2341–60.PubMedCrossRefGoogle Scholar
  15. Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW. A DNA structural atlas for Escherichia coli. J Mol Biol. 2000;299(4):907–30.PubMedCrossRefGoogle Scholar
  16. Satchwell SC, Drew HR, Travers AA. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986;191(4):659–75.PubMedCrossRefGoogle Scholar
  17. Shpigelman ES, Trifonov EN, Boishoy A. Curvature: software for the analysis of curved DNA. Comput Appl Biosci. 1993;9:435–40.PubMedGoogle Scholar
  18. Strom SL, Brahamsha B, Fredrickson KA, Apple JK, Rodr’iguez AG. A giant cell surface protein in Synechococcus WH8102 inhibits feeding by a dinoflagellate predator. Environ Microbiol. 2012;14(3):807–16.PubMedCrossRefGoogle Scholar
  19. Sun S, Chen J, Li W, et al. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res. 2011;39(Database issue):D546–51.PubMedCentralPubMedCrossRefGoogle Scholar
  20. Tringe SG, von Mering C, Kobayashi A, et al. Comparative metagenomics of microbial communities. Science. 2005;308(5721):554–7.PubMedCrossRefGoogle Scholar
  21. Tripp HJ, Kitner JB, Schwalbach MS, et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature. 2008;452(7188):741–4.PubMedCrossRefGoogle Scholar
  22. Tyson GW, Chapman J, Hugenholtz P, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428(6978):37–43.PubMedCrossRefGoogle Scholar
  23. Yooseph S, Sutton G, Rusch DB, et al. The Sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol. 2007;5(3):e16.PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
  2. 2.Center for Biological Sequence Analysis, Department of Systems BiologyTechnical University of DenmarkKongens LyngbyDenmark