Abstract
The trend of recent researches, in which synthetic biology and white technology through system approaches based on “Omics technology” are recognized as the ground of biotechnology, indicates the coming of the ‘metagenome era’ that accesses the genomes of all microbes aiming at the understanding and industrial application of the whole microbial resources. The remarkable advance of technologies for digging out and analyzing metagenome is enabling not only practical applications of metagenome but also system approaches on a mixed-genome level based on accumulated information. In this situation, the present review is purposed to introduce the trends and methods of research on metagenome and to examine big science led by related resources in the future.
Keywords: Metagenome, Gene mining, Novel metabolites, Systems approach, Biological treasure
Full Text
The Full Text of this article is available as a PDF (824.8 KB).
References
- 1.Hunter-Cevera J.C. The value of microbial diversity. Curr Opin Microbiol. 1998;1:278–285. doi: 10.1016/S1369-5274(98)80030-1. [DOI] [PubMed] [Google Scholar]
- 2.Eisen J.A. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol. 2007;5:e82. doi: 10.1371/journal.pbio.0050082. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Zwolinski M.D. DNA sequencing: Strategies for soil microbiology. Soil Sci Am J. 2007;71:592–600. doi: 10.2136/sssaj2006.0125. [DOI] [Google Scholar]
- 4.Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669–685. doi: 10.1128/MMBR.68.4.669-685.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Bull A.T., Ward A.C., Goodfellow M. Search and discovery strategies for biotechnology: The paradigm shift. Microbiol Mol Biol Rev. 2000;64:573–606. doi: 10.1128/MMBR.64.3.573-606.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Xu J.P. Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol. 2006;15:1713–1731. doi: 10.1111/j.1365-294X.2006.02882.x. [DOI] [PubMed] [Google Scholar]
- 7.Torsvik V.L. Isolation of bacterial DNA from soil. Soil Biol Biochem. 1980;12:15–21. doi: 10.1016/0038-0717(80)90097-8. [DOI] [Google Scholar]
- 8.Ferrer M., Beloqui A., Golyshin P.N. Microbial metagenomes: moving forward industrial biotechnology. J Chem Technol Biotechnol. 2007;82:421–423. doi: 10.1002/jctb.1695. [DOI] [Google Scholar]
- 9.Ferrer M., Martinez-Abarca F., Golyshin P.N. Mining genomes and ‘metagenomes’ for novel catalysts. Curr Opin Biotechnol. 2005;16:588–593. doi: 10.1016/j.copbio.2005.09.001. [DOI] [PubMed] [Google Scholar]
- 10.Kowalchuk G.A., Speksnijder A.G., Zhang K., Goodman R.M., Veen J.A. Finding the needles in the metagenome haystack. Microb Ecol. 2007;53:475–485. doi: 10.1007/s00248-006-9201-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Field D., Kyrpides N. The positive role of the ecological community in the genomic revolution. Microb Ecol. 2007;53:507–511. doi: 10.1007/s00248-007-9206-5. [DOI] [PubMed] [Google Scholar]
- 12.Park S.H., Cheong D.E., Lee J.Y., Han S.S., Lee J.H., Kim G.J. Analyses of the structural organization of unidentified open reading frames from metagenome. Biochem Biophys Res Commun. 2007;356:961–967. doi: 10.1016/j.bbrc.2007.03.090. [DOI] [PubMed] [Google Scholar]
- 13.Kim B.S., Kim S.Y., Park J., Park W., Hwang K.Y., Yoon Y.J., Oh W.K., Kim B.Y., Ahn J.S. Sequence-based screening for self-sufficient P450 monooxygenase from a metagenome library. J Appl Microbiol. 2007;102:1392–400. doi: 10.1111/j.1365-2672.2006.03169.x. [DOI] [PubMed] [Google Scholar]
- 14.Jiang C., Wu B. Molecular cloning and functional characterization of a novel decarboxylase from uncultured microorganisms. Biochem Biophys Res Commun. 2007;357:421–426. doi: 10.1016/j.bbrc.2007.03.159. [DOI] [PubMed] [Google Scholar]
- 15.Brady S.F., Bauer J.D., Clarke-Pearson M.F., Daniels R. Natural products from isnA-containing biosynthetic gene clusters recovered from the genomes of cultured and uncultured bacteria. J Am Chem Soc. 2007;129:12102–12103. doi: 10.1021/ja075492v. [DOI] [PubMed] [Google Scholar]
- 16.Price N.D., Papin J.A., Schilling C.H., Palsson B.O. Genome-scale microbial in silico models: the constraintsbased approach. Trends Biotechnol. 2003;21:162–169. doi: 10.1016/S0167-7799(03)00030-1. [DOI] [PubMed] [Google Scholar]
- 17.Beja O., Aravind L., Koonin E.V., Suzuki M.T., Hadd A., Nguyen L.P., Jovanovich S.B., Gates C.M., Feldman R.A., Spudich J.L., Spudich E.N., DeLong E.F. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 2000;289:1902–1906. doi: 10.1126/science.289.5486.1902. [DOI] [PubMed] [Google Scholar]
- 18.Tyson G.W., Chapman J., Hugenholtz P., Allen E.E., Ram R.J., Richardson P.M., Solovyev V.V., Rubin E.M., Rokhsar D.S., Banfield J.F. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37–43. doi: 10.1038/nature02340. [DOI] [PubMed] [Google Scholar]
- 19.Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., Fouts D.E., Levy S., Knap A.H., Lomas M.W., Nealson K., White O., Peterson J., Hoffman J., Parsons R., Baden-Tillson H., Pfannkoch C., Rogers Y.H., Smith H.O. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304:66–74. doi: 10.1126/science.1093857. [DOI] [PubMed] [Google Scholar]
- 20.Gill S.R., Pop M., Deboy R.T., Eckburg P.B., Turnbaugh P.J., Samuel B.S., Gordon J.I., Relman D.A., Fraser-Liggett C.M., Nelson K.E. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–1359. doi: 10.1126/science.1124234. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21.Garcia Martin H., Ivanova N., Kunin V., Warnecke F., Barry K.W., McHardy A.C., Yeates C., He S., Salamov A.A., Szeto E., Dalin E., Putnam N.H., Shapiro H.J., Pangilinan J.L., Rigoutsos I., Kyrpides N.C., Blackall L.L., McMahon K.D., Hugenholtz P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol. 2006;24:1263–1269. doi: 10.1038/nbt1247. [DOI] [PubMed] [Google Scholar]
- 22.Koonin E.V. Metagenomic sorcery and the expanding protein universe. Nat Biotechnol. 2007;25:540–542. doi: 10.1038/nbt0507-540. [DOI] [PubMed] [Google Scholar]
- 23.Abe T., Sugawara H., Kinouchi M., Kanaya S., Ikemura T. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res. 2005;12:281–290. doi: 10.1093/dnares/dsi015. [DOI] [PubMed] [Google Scholar]
- 24.McHardy A.C., Martin H.G., Tsirigos A., Hugenholtz P., Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods. 2007;4:63–72. doi: 10.1038/nmeth976. [DOI] [PubMed] [Google Scholar]
- 25.Jean-Philippe G., Jean-Louis R. Enzyme assays for high-throughput screening. Current Opinion in Biotechnology. 2004;15:314–322. doi: 10.1016/j.copbio.2004.06.008. [DOI] [PubMed] [Google Scholar]
- 26.Hu Y., Chen G.Y.J., Yao S.Q. Activity-based high-throughput screening of enzymes by using a DNA microarray. Angew Chem Int Ed. 2005;44:1048–1053. doi: 10.1002/anie.200461612. [DOI] [PubMed] [Google Scholar]
- 27.Li Y.G., Wexler M., Richardson D.J., Bond P.L., Johnston A.W. Screening a wide host-range, waste-water metagenomic library in tryptophan auxotrophs of Rhizobium leguminosarum and of Escherichia coli reveals different classes of cloned trp genes. Environ Microbiol. 2005;7:1927–1936. doi: 10.1111/j.1462-2920.2005.00853.x. [DOI] [PubMed] [Google Scholar]
- 28.Lee D., Redfern O., Orengo C. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol. 2007;8:995–1005. doi: 10.1038/nrm2281. [DOI] [PubMed] [Google Scholar]
- 29.Markowitz V.M., Ivanova N., Palaniappan K., Szeto E., Korzeniewski F., Lykidis A., Anderson I., Mavromatis K., Kunin V., Garcia Martin H., Dubchak I., Hugenholtz P., Kyrpides N.C. An experimental metagenome data management and analysis system. Bioinformatics. 2006;22:e359–367. doi: 10.1093/bioinformatics/btl217. [DOI] [PubMed] [Google Scholar]
- 30.Mavromatis K., Ivanova N., Barry K., Shapiro H., Goltsman E., McHardy A.C., Rigoutsos I., Salamov A., Korzeniewski F., Land M., Lapidus A., Grigoriev I., Richardson P., Hugenholtz P., Kyrpides N.C. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007;4:495–500. doi: 10.1038/nmeth1043. [DOI] [PubMed] [Google Scholar]
- 31.Havre SL, Webb-Robertson BJ, Shah A, Posse C, Gopalan B and Brockman FJ (2005) Bioinformatic insights from metagenomics through visualization. Proc IEEE Comput Syst Bioinform Conf, pp 341–350 [DOI] [PubMed]
- 32.Warnecke F., Luginbühl P., Ivanova N., Ghassemian M., Richardson T.H., Stege J.T., Cayouette M., McHardy A.C., Djordjevic G., Aboushadi N., Sorek R., Tringe S.G., Podar M., Martin H.G., Kunin V., Dalevi D., Madejska J., Kirton E., Platt D., Szeto E., Salamov A., Barry K., Mikhailova N., Kyrpides N.C., Matson E.G., Ottesen E.A., Zhang X., Hernández M., Murillo C., Acosta L.G., Rigoutsos I., Tamayo G., Green B.D., Chang C., Rubin E.M., Mathur E.J., Robertson D.E., Hugenholtz P., Leadbetter J.R. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450:560–565. doi: 10.1038/nature06269. [DOI] [PubMed] [Google Scholar]
- 33.Krsek M., Wellington E.M. Comparison of different methods for the isolation and purification of total community DNA from soil. J Microbiol Methods. 1999;39:1–16. doi: 10.1016/S0167-7012(99)00093-7. [DOI] [PubMed] [Google Scholar]
- 34.Frostegard A., Courtois S., Ramisse V., Clerc S., Bernillon D., Gall F., Jeannin P., Nesme X., Simonet P. Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol. 1999;65:5409–5420. doi: 10.1128/aem.65.12.5409-5420.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 35.Miller D.N., Bryant J.E., Madsen E.L., Ghiorse W.C. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol. 1999;65:4715–4724. doi: 10.1128/aem.65.11.4715-4724.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 36.Neufeld J.D., Dumont M.G., Vohra J., Murrell J.C. Methodological considerations for the use of stable isotope probing in microbial ecology. Microb Ecol. 2006;53:435–442. doi: 10.1007/s00248-006-9125-x. [DOI] [PubMed] [Google Scholar]
- 37.Schloss P.D., Handelsman J. Biotechnological prospects from metagenomics. Curr Opin Biotechnol. 2003;14:303–310. doi: 10.1016/S0958-1669(03)00067-3. [DOI] [PubMed] [Google Scholar]
- 38.Ohuchi S., Nakano H., Yamane T. In vitro method for the generation of protein libraries using PCR amplification of a single DNA molecule and coupled transcription/translation. Nucleic Acids Res. 1998;26:4339–4346. doi: 10.1093/nar/26.19.4339. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 39.Yu W.H., Su S.C., Lee C.Y. A novel retrieval system for nearly complete microbial genomic fragments from soil samples. J Microbiol Methods. 2008;72:197–205. doi: 10.1016/j.mimet.2007.11.022. [DOI] [PubMed] [Google Scholar]
- 40.Nesbø C.L., Boucher Y., Dlutek M., Doolittle W.F. Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environ Microbiol. 2005;7:2011–2026. doi: 10.1111/j.1462-2920.2005.00918.x. [DOI] [PubMed] [Google Scholar]
- 41.Berry A.E., Chiocchini C., Selby T., Sosio M., Wellington E.M. Isolation of high molecular weight DNA from soil for cloning into BAC vectors. FEMS Microbiol Lett. 2003;223:15–20. doi: 10.1016/S0378-1097(03)00248-9. [DOI] [PubMed] [Google Scholar]
- 42.Huson D.H., Auch A.F., Qi J., Schuster S.C. MEGAN analysis of metagenomic data. Genome Res. 2007;17:377–386. doi: 10.1101/gr.5969107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 43.Gabor E.M., Vries E.J., Janssen D.B. Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. Environ Microbiol. 2004;6:948–958. doi: 10.1111/j.1462-2920.2004.00643.x. [DOI] [PubMed] [Google Scholar]
- 44.Cowan D., Meyer Q., Stafford W., Muyanga S., Cameron R., Wittwer P. Metagenomic gene discovery: past, present and future. Trends Biotechnol. 2005;23:321–329. doi: 10.1016/j.tibtech.2005.04.001. [DOI] [PubMed] [Google Scholar]
- 45.Galvão T.C., Mohn W.W., Lorenzo V. Exploring the microbial biodegradation and biotransformation gene pool. Trends Biotechnol. 2005;23:497–506. doi: 10.1016/j.tibtech.2005.08.002. [DOI] [PubMed] [Google Scholar]
- 46.Terpe K. Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol. 2006;72:211–222. doi: 10.1007/s00253-006-0465-8. [DOI] [PubMed] [Google Scholar]
- 47.Uchiyama T., Abe T., Ikemura T., Watanabe K. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol. 2005;23:88–93. doi: 10.1038/nbt1048. [DOI] [PubMed] [Google Scholar]
- 48.Yun J., Ryu S. Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb Cell Fact. 2005;4:8. doi: 10.1186/1475-2859-4-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 49.Lorenz P., Liebeton K., Niehaus F., Eck J. Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Curr Opin Biotechnol. 2002;13:572–577. doi: 10.1016/S0958-1669(02)00345-2. [DOI] [PubMed] [Google Scholar]
- 50.Petri R., Schmidt-Dannert C. Dealing with complexity: evolutionary engineering and genome shuffling. Curr Opin Biotechnol. 2004;15:298–304. doi: 10.1016/j.copbio.2004.05.005. [DOI] [PubMed] [Google Scholar]
- 51.Oh H.J., Cho K.W., Jung I.S., Kim W.H., Hur B.K., Kim G.J. Expanding functional spaces of enzymes by utilizing whole genome treasure for library construction. J Mol Catal B-enzymatic. 2003;26:241–250. doi: 10.1016/j.molcatb.2003.06.007. [DOI] [Google Scholar]
- 52.Lorenz P., Eck J. Metagenomics and industrial applications. Nat Rev Microbiol. 2005;3:510–516. doi: 10.1038/nrmicro1161. [DOI] [PubMed] [Google Scholar]
- 53.Ferrer M., Beloqui A., Golyshin P.N. Microbial metagenomes: moving forward industrial biotechnology. Chem Technol Biotechnol. 2007;82:421–423. doi: 10.1002/jctb.1695. [DOI] [Google Scholar]
- 54.Welbaum G.E., Sturz A.V., Dong Z.M., Nowak J. Managing soil microorganisms to improve productivity of agro-ecosystems. Crit Rev Plant Sci. 2004;23:175–193. doi: 10.1080/07352680490433295. [DOI] [Google Scholar]
- 55.Tsai S.H., Liu C.P., Yang S.S. Microbial conversion of food wastes for biofertilizer production with thermophilic lipolytic microbes. Renew Energy. 2007;32:904–915. doi: 10.1016/j.renene.2006.04.019. [DOI] [Google Scholar]
- 56.Dethlefsen L., McFall-Ngai M., Relman D.A. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007;449:811–818. doi: 10.1038/nature06245. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 57.Zoetendal E.G., Vaughan E.E., Vos W.M. A microbial world within us. Mol Microbiol. 2006;59:1639–1650. doi: 10.1111/j.1365-2958.2006.05056.x. [DOI] [PubMed] [Google Scholar]
- 58.Martínez J.L., Baquero F., Andersson D.I. Predicting antibiotic resistance. Nat Rev Microbiol. 2007;5:958–965. doi: 10.1038/nrmicro1796. [DOI] [PubMed] [Google Scholar]
- 59.Courtois S., Cappellano C.M., Ball M., Francou F.X., Normand P., Helynck G., Martinez A., Kolvek S.J., Hopke J., Osburne M.S., August P.R., Nalin R., Guérineau M., Jeannin P., Simonet P., Pernodet J.L. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol. 2003;69:49–55. doi: 10.1128/AEM.69.1.49-55.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 60.Li X., Qin L. Metagenomics-based drug discovery and marine microbial diversity. Trends Biotechnol. 2005;23:539–543. doi: 10.1016/j.tibtech.2005.08.006. [DOI] [PubMed] [Google Scholar]
- 61.D’Costa V.M., Griffiths E., Wright G.D. Expanding the soil antibiotic resistome: exploring environmental diversity. Curr Opin Microbiol. 2007;10:481–489. doi: 10.1016/j.mib.2007.08.009. [DOI] [PubMed] [Google Scholar]
- 62.Pontes D.S., Lima-Bittencourt C.I., Chartone-Souza E., Amaral Nascimento A.M. Molecular approaches: advantages and artifacts in assessing bacterial diversity. J Ind Microbiol Biotechnol. 2007;34:463–473. doi: 10.1007/s10295-007-0219-3. [DOI] [PubMed] [Google Scholar]
- 63.Maron P.A., Ranjard L., Mougel C., Lemanceau P. Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol. 2007;53:486–493. doi: 10.1007/s00248-006-9196-8. [DOI] [PubMed] [Google Scholar]
- 64.Cook K.L., Sayler G.S. Environmental application of array technology: promise, problems and practicalities. Curr Opin Biotechnol. 2003;14:311–318. doi: 10.1016/S0958-1669(03)00057-0. [DOI] [PubMed] [Google Scholar]
- 65.Mashego M.R., Rumbold K., Mey M., Vandamme E., Soetaert W., Heijnen J.J. Microbial metabolomics: past, present and future methodologies. Biotechnol Lett. 2007;29:1–16. doi: 10.1007/s10529-006-9218-0. [DOI] [PubMed] [Google Scholar]
- 66.Danchin A. The bag or the spindle: the cell factory at the time of systems’ biology. Microb Cell Fact. 2004;3:13. doi: 10.1186/1475-2859-3-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 67.Glass J.I., Assad-Garcia N., Alperovich N., Yooseph S., Lewis M.R., Maruf M., Hutchison C.A., 3rd, Smith H.O., Venter J.C. Essential genes of a minimal bacterium. Proc Natl Acad Sci USA. 2006;103:425–430. doi: 10.1073/pnas.0510013103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 68.Lartigue C., Glass J.I., Alperovich N., Pieper R., Parmar P.P., Hutchison C.A., 3rd, Smith H.O., Venter J.C. Genome transplantation in bacteria: changing one species to another. Science. 2007;317:632–638. doi: 10.1126/science.1144622. [DOI] [PubMed] [Google Scholar]
- 69.Gabor E., Liebeton K., Niehaus F., Eck J., Lorenz P. Updating the metagenomics toolbox. Biotechnol J. 2007;2:201–206. doi: 10.1002/biot.200600250. [DOI] [PubMed] [Google Scholar]
- 70.Atsumi S., Hanai T., Liao J.C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature. 2008;451:86–89. doi: 10.1038/nature06450. [DOI] [PubMed] [Google Scholar]