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Which Microbial Communities Are Present? Sequence-Based Metagenomics

  • Sean M. Caffrey
Conference paper

Abstract

The use of metagenomic methods that directly sequence environmental samples has revealed the extraordinary microbial diversity missed by traditional culture-based methodologies. Therefore, to develop a complete and representative model of an environment’s microbial community and activities, metagenomic analysis is an essential tool.

Keywords

Microbial Community Metagenomic Sequencing Ocean Surface Water Longe Read Length Acid Mine Drainage Environment 
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.

References

  1. Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, Chang HW, Watson D, Brodie EL, Hazen TC et al (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72:3291–3301CrossRefGoogle Scholar
  2. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 3:e2836CrossRefGoogle Scholar
  3. Badger JH, Olsen GJ (1999) CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 16:512–524CrossRefGoogle Scholar
  4. Besemer J, Borodovsky M (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27:3911–3920CrossRefGoogle Scholar
  5. Bohannan BJ, Hughes J (2003) New approaches to analyzing microbial biodiversity data. Curr Opin Microbiol 6:282–287CrossRefGoogle Scholar
  6. Callaway TR, Dowd SE, Wolcott RD, Sun Y, McReynolds JL, Edrington TS, Byrd JA, Anderson RC, Krueger N, Nisbet DJ (2009) Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing. Pollut Sci 88:298–302Google Scholar
  7. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM et al (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145CrossRefGoogle Scholar
  8. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641CrossRefGoogle Scholar
  9. Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B (1999) Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol 16:1391–1399CrossRefGoogle Scholar
  10. Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS (2008) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8:125CrossRefGoogle 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 7:57CrossRefGoogle Scholar
  12. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105:3805–3810CrossRefGoogle Scholar
  13. Frishman D, Mironov A, Mewes HW, Gelfand M (1998) Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res 26:2941–2947CrossRefGoogle Scholar
  14. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5:235–237CrossRefGoogle Scholar
  15. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100CrossRefGoogle Scholar
  16. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8:R143CrossRefGoogle Scholar
  17. Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386CrossRefGoogle Scholar
  18. Karlin S, Mrazek J, Campbell AM (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179:3899–3913Google Scholar
  19. Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide to metagenomics. Microbial Mol Biol Rev 72:557–578Google Scholar
  20. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235CrossRefGoogle Scholar
  21. Lueders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320–326CrossRefGoogle Scholar
  22. MacLean D, Jones JD, Studholme DJ (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev Microbiol 7:287–296Google Scholar
  23. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402CrossRefGoogle Scholar
  24. Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53:486–493CrossRefGoogle Scholar
  25. McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 4:63–72CrossRefGoogle Scholar
  26. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A et al (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386CrossRefGoogle Scholar
  27. Miller SR, Strong AL, Jones KL, Ungerer MC (2009) Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone National Park. Appl Environ Microbiol 75:4565–4572CrossRefGoogle Scholar
  28. Moreno-Paz M, Parro V (2006) Amplification of low quantity bacterial RNA for microarray studies: time-course analysis of Leptospirillum ferrooxidans under nitrogen-fixing conditions. Environ Microbiol 8:1064–1073CrossRefGoogle Scholar
  29. Noguchi H, Park J, Takagi T (2006) MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 34:5623–5630CrossRefGoogle Scholar
  30. Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, Plant RN, Egholm M, Rothberg JM, Leamon JH (2006) Assessment of whole genome amplification – induced bias through high – throughput, massively parallel whole genome sequencing. BMC Genomics 7:216Google Scholar
  31. Raes J, Foerstner KU, Bork P (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol 10:490–498CrossRefGoogle Scholar
  32. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506CrossRefGoogle Scholar
  33. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C (2003) Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res 13:216–223CrossRefGoogle Scholar
  34. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145CrossRefGoogle Scholar
  35. Shi Y, Tyson GW, DeLong EF (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column. Nature 459:266–269CrossRefGoogle Scholar
  36. 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 103:12115–12120CrossRefGoogle Scholar
  37. Teeling H, Meyerdierks A, Bauer M, Amann R, Glockner FO (2004) Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 6:938–947CrossRefGoogle Scholar
  38. Tringe SG, Hugenholtz P (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11:442–446CrossRefGoogle Scholar
  39. Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6:805–814CrossRefGoogle Scholar
  40. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC et al (2005) Comparative metagenomics of microbial communities. Science 308:554–557CrossRefGoogle Scholar
  41. 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 428:37–43CrossRefGoogle Scholar
  42. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74CrossRefGoogle Scholar
  43. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271Google Scholar
  44. Wommack KE, Bhavsar J, Ravel J (2008) Metagenomics: read length matters. Appl Environ Microbiol 74:1453–1463CrossRefGoogle Scholar
  45. Youssef N, Sheik C, Krumholz L, Najar F, Roe B, Elshahed M (2009) A Comparative study of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol 75:5227–5236CrossRefGoogle Scholar

Copyright information

© Springer Netherlands 2010

Authors and Affiliations

  1. 1.Genome AlbertaCalgaryCanada

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