Metagenomics

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.

See also

• Microbiome
• Genomes OnLine Database (GOLD)

Further reading

Books

• The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet, by The Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007). ISBN 978-0-309-10676-4.

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

• Huson, D.H., A. Auch, Ji Qi and S.C. Schuster, MEGAN Analysis of Metagenomic Data, Genome Research. 17:377-386, 2007
• Krause L, Diaz NN, Bartels D, Edwards RA, Puhler A, Rohwer F, Meyer F, Stoye J. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics. 2006 15;22(14):e281-9.
• Rodriguez-Brito B, Rohwer F, Edwards RA. An application of statistics to comparative metagenomics. BMC Bioinformatics. 2006 20;7:162.
• Raes, J., Foerstner, K.U. & Bork, P. (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol, in press.
• Harrington, E.D., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., Raes, J. & Bork, P. (2007) Quantitative assessment of protein function predicion from metagenomics shotgun sequences. Proc. Natl. Acad. Sci. USA 104, 13913-8
• Tress, M. L. et al. (2006). An analysis of the Sargasso Sea resource and the consequences for database composition. Bmc Bioinformatics 7
• Foerstner KU, von Mering C, Hooper SD, Bork P (2005) Environments shape the nucleotide composition of genomes. EMBO Rep. 6(12): 1208-13
• Raes, J., Korbel, J.O., Lercher, M.J., Von Mering, C. & Bork, P. (2007) Prediction of effective genome size in metagenomic samples. Genome Biology 8, R10 [1]
• von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., Ward N. & Bork, P. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315, 1126-1130
• Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 4(6):495-500
• Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavromatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC. (2006) An experimental metagenome data management and analysis system. Bioinformatics. 22(14):e359-67
• Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. (2007) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. Epub

Marine ecosystems

• Angly, F. E. et al. (2006). The marine viromes of four oceanic regions. PloS Biology 4: 2121-31.
• Beja, O. et al. (2000). Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289: 1902-6.
• Beja, O. et al. (2001). Proteorhodopsin phototrophy in the ocean. Nature 411: 786-9.
• 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.

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

• 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

External links

• 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
• wikipedia:Metagenomics