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.
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.
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- Beja, O. et al. (2002). Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-3.
- Culley, A. I. et al. (2006). Metagenomic analysis of coastal RNA virus communities. Science 312: 1795-8.
- DeLong, E. F. et al. (2006). Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
- Hallam, S. J. et al. (2006). Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proceedings of the National Academy of Sciences of the United States of America 103: 18296-301.
- John, D. E. et al. (2006). Gene diversity and organization in rbcL-containing genome fragments from uncultivated Synechococcus in the Gulf of Mexico. Marine Ecology-Progress Series 316: 23-33.
- Kannan N. et al. (2007). Structural and Functional Diversity of the Microbibial Kinome. PloS Biology 5: 467-478
- Rusch D. B. et al. (2007). The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PloS Biology 5: 398-431
- Tringe, S. G. et al. (2005). Comparative metagenomics of microbial communities. Science 308: 554-7.
- Woyke, T. et al. (2006). Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443: 950-5.
- Yooseph S. et al. (2007). The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. 'PloS Biology 5: 432-466
- Yutin, N. & Beja, O. (2005). Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics. Environmental Microbiology 7: 2027-33.
- 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, 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.
- 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.
- H. N. Poinar, C. Schwarz, Ji Qi, B. Shapiro, R. D. E. MacPhee, B. Buigues, A. Tikhonov, D. H. Huson, L. P. Tomsho, A. Auch, M. Rampp, W. Miller, S. C. Schuster, Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA, Science 311:392-394, 2006
- MEGAN MEtaGenome ANalyzer. A stand-alone metagenome analysis tool.
- Metagenomics and Our Microbial Planet A website on metagenomics and the vital role of microbes on Earth from the National Academies.
- The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet A report released by the National Research Council in March 2007. Also, see the Report In Brief.
- IMG/M The Integrated Microbial Genomes system, for metagenome analysis by the DOE-JGI.
- CAMERA Cyberinfrastructure for Metagenomics, data repository and tools for metagenomics research.
- A good overview of metagenomics from the Science Creative Quarterly
- list of Metagenome Projects from genomesonline.org
- The SEED publicly available, free, metagenomics annotation pipeline for pyrosequences, Sanger sequences, and other sequence approaches.
- Human microbiome project
- MetaHIT official website for the EU-funded project : Metagenomics of the Human Intestinal Tract
- Annotathon Bioinformatics Training Through Metagenomic Sequence Annotation