Difference between revisions of "Metagenomics"

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Metagenomics is the study of the DNA from all the genomes in an environment. The term ''meta'' implies that this transcends traditional genomics. Most of the bacteria living in an environment will not grow in standard laboratory media. This is true for more than 99% of the species present in a typical soil sample, and similar numbers are likely to hold for bacteria growing in different environmental niches. Thus, by sampling all of the DNA from a given environment, it is possible to gain much additional information that would not be available from traditional methods that depend on single, pure monocultures of a well-characterized bacterium. The area of metagenomics is relatively new and rapidly changes as technology allows more and better sampling of the environmental DNA. The consequences of current improvements in speed and output of genome technology to future research are discussed.<ref>David Wayne Ussery, Trudy M. Wassenaar, Stefano Borini (2009). ''Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists''. Springer. ISBN 978-1849967631.</ref>
 
Metagenomics is the study of the DNA from all the genomes in an environment. The term ''meta'' implies that this transcends traditional genomics. Most of the bacteria living in an environment will not grow in standard laboratory media. This is true for more than 99% of the species present in a typical soil sample, and similar numbers are likely to hold for bacteria growing in different environmental niches. Thus, by sampling all of the DNA from a given environment, it is possible to gain much additional information that would not be available from traditional methods that depend on single, pure monocultures of a well-characterized bacterium. The area of metagenomics is relatively new and rapidly changes as technology allows more and better sampling of the environmental DNA. The consequences of current improvements in speed and output of genome technology to future research are discussed.<ref>David Wayne Ussery, Trudy M. Wassenaar, Stefano Borini (2009). ''Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists''. Springer. ISBN 978-1849967631.</ref>
 
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==See also==
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*[[Microbiome]]
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*[[Genomes OnLine Database]] (GOLD)
  
 
==References==
 
==References==

Revision as of 23:05, 23 July 2012

Metagenomics (also Environmental Genomics, Ecogenomics or Community Genomics) is the study of genetic material recovered directly from environmental samples. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures. This relatively new field of genetic research enables studies of organisms that are not easily cultured in a laboratory as well as studies of organisms in their natural environment.

I did some research in metagenomics whilst in Denmark.

Overview

Metagenomics is the study of the DNA from all the genomes in an environment. The term meta implies that this transcends traditional genomics. Most of the bacteria living in an environment will not grow in standard laboratory media. This is true for more than 99% of the species present in a typical soil sample, and similar numbers are likely to hold for bacteria growing in different environmental niches. Thus, by sampling all of the DNA from a given environment, it is possible to gain much additional information that would not be available from traditional methods that depend on single, pure monocultures of a well-characterized bacterium. The area of metagenomics is relatively new and rapidly changes as technology allows more and better sampling of the environmental DNA. The consequences of current improvements in speed and output of genome technology to future research are discussed.[1]

See also

References

  1. ↑ David Wayne Ussery, Trudy M. Wassenaar, Stefano Borini (2009). Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists. Springer. ISBN 978-1849967631.

Further reading

Review articles

  • Edwards RA, & Rohwer F. "Viral metagenomics". Nat Rev Microbiol. 2005 3(6):504-10. PubMed
  • Eisen, J. A. (2007). Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5(3): e82
  • Green, B. D. & Keller, M. (2006). Capturing the uncultivated majority. Current Opinion in Biotechnology 17[3], 236-240.
  • Handelsman J. (2004). Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews 68:669-685.
  • Keller, M. & Sengler, K. (2004). Tapping into microbial diversity. Nature Reviews Microbiology 2[2], 141-150.
  • Lombard, N. et al. (2006). The metagenomics of microbial communities. Biofutur 24-7.
  • Riesenfeld, C. S. et al. (2004). Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38: 525-52.
  • Rodriguez Valera, F. (2002). Approaches to prokaryotic biodiversity: a population genetics perspective. Environmental Microbiology 4: 628-33.
  • Rodriguez-Valera. (2004). Environmental genomics, the big picture?. FEMS Microbiology Letters 231:153-158.
  • Torsvik, V. & Ovreas, L. (2002). Microbial diversity and function in soil: from genes to ecosystems. Current opinion in Microbiology 5: 240-5.
  • Whitaker, R. J. & Banfield, J. F. (2006). Population genomics in natural microbial communities. Trends in Ecology & Evolution 21: 508-16.
  • Worden, A. Z. et al. (2006). In-depth analyses of marine microbial community genomics. Trends in Microbiology 14: 331-6.
  • Xu, J. P. (2006). Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Molecular Ecology 15: 1713-31.

Methods

  • Beja, O. et al. (2000). Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environmental Microbiology 2: 516-29.
  • Sebat, J. L. et al. (2003). Metagenomic profiling: Microarray analysis of an environmental genomic library. Applied and Environmental Microbiology 69: 4927-34.
  • Suzuki, M. T. et al. (2004). Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microbial Ecology 48: 473-88.

Bioinformatics

Marine ecosystems

Sediments

  • Abulencia, C. B., Wyborski, D. L., Garcia, J. A., Podar, M., Chen, W., Chang, S. H. et al. (2006). Environmental whole-genome amplification to access microbial populations in contaminated sediments. Applied and Environmental Microbiology 72[5], 3291-3301.
  • Breitbart et al. (2004). Diversity and population structure of a nearshore marine sediment viral community. Proceedings of the Royal Society B 271: 565-574.

Extreme environments

  • Baker, B. J. et al. (2006). Lineages of acidophilic archaea revealed by community genomic analysis. Science 314: 1933-5.

Medical Sciences and biotechnological applications

  • Breitbart et al. (2003). Metagenomic analyses of an uncultured viral community from human feces. Journal of Bacteriology 185:6220-6223.
  • Breitbart, M. and Rohwer, F. (2005) Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. BioTechniques, 39, 729-736.
  • Gill, S. R. et al. (2006). Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-9.
  • Mathur, E., Toledo, G., Green, B. D., Podar, M., Richardson, T. H., Kulwiec (2005). A biodiversity-based approach to development of performance enzymes: Applied metagenomics and directed evolution. Industrial Biotechnology, 1, 283-287.
  • Schloss, P. D. & Handelsman, J. (2003). Biotechnological prospects from metagenomics. Current Opinion in Biotechnology 14: 303-10.
  • Zengler, K., Paradkar, A., & Keller, M. (2005). New methods to access microbial diversity for small molecule discovery. Natural Products , 275-293.
  • Zhang, T., Breitbart, M., Lee, W.H., Run, J.Q., Wei, C.L., Soh, S.W., Hibberd, M.L., Liu, E.T., Rohwer, F. and Ruan, Y. (2006) RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS biology, 4, e3.

Ancient DNA

External links

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