Biopolym. Cell. 2008; 24(3):199-211.
http://dx.doi.org/10.7124/bc.0007A1
Огляди
Метагеномний аналіз для мікробної екології і біотехнології
1Овчаренко Л. П., 1Козировська Н. О.
  1. Інститут молекулярної біології і генетики НАН України
    Вул. Академіка Заболотного, 150, Київ, Україна, 03680

Abstract

Метагеноміка вивчає сукупність геномів мікроорганізмів довкілля методами молекулярної генетики та інших галузей біологічної науки (біоінформатика, протеоміка, метаболоміка). Метагеномний аналіз дає можливість реконструювати мікробні угруповання, у тому числі некультивованих мікроорганізмів, практично будь-яких екосистем, визначити їхні функції, взаємини з макроорганізмами тощо. У найближчі роки ключовим у метагеноміці буде пошук нових генів для біотехнологічної та фармацевтичної промисловості.
Keywords: метагеноміка, мікробна екологія, спільноти мікроорганізмів
Повний текст: (PDF, українською)

References

[1] Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68(4):669-85.
[2] Torsvik V, Daae FL, Sandaa RA, Ovreas L. Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol. 1998;64(1):53-62.
[3] Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977;74(12):5463-7.
[4] Stahl DA, Lane DJ, Olsen GJ, Pace NR. Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science. 1984;224(4647):409-11.
[5] Hugenholtz P, Pace NR. Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol. 1996;14(6):190-7.
[6] Zuckerkandl E, Pauling L. Molecules as documents of evolutionary history. J Theor Biol. 1965;8(2):357-66.
[7] Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol. 2007;45(9):2761-4.
[8] Steffan RJ, Atlas RM. DNA amplification to enhance detection of genetically engineered bacteria in environmental samples. Appl Environ Microbiol. 1988;54(9):2185-91.
[9] Laguerre G, Allard MR, Revoy F, Amarger N. Rapid Identification of Rhizobia by Restriction Fragment Length Polymorphism Analysis of PCR-Amplified 16S rRNA Genes. Appl Environ Microbiol. 1994;60(1):56-63.
[10] De Boer S. N., Copeman R. J. Endophytic bacterial flora in Solanum tuberosum and its significance in bacterial ring root disease. Can. J. Plant Sci. 1974; 54(1):115–122.
[11] Fisher MM, Triplett EW. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol. 1999;65(10):4630-6.
[12] Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993;59(3):695-700.
[13] Liu WT, Marsh TL, Cheng H, Forney LJ. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol. 1997;63(11):4516-22.
[14] Xiao W, Oefner PJ. Denaturing high-performance liquid chromatography: A review. Hum Mutat. 2001;17(6):439-74.
[15] Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol. 2007;144(1):32-42.
[16] Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437(7057):376-80.
[17] Ahmadian A, Ehn M, Hober S. Pyrosequencing: history, biochemistry and future. Clin Chim Acta. 2006;363(1-2):83-94.
[18] Mitra RD, Church GM. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 1999;27(24):e34.
[19] Lagerqvist J, Zwolak M, Di Ventra M. Fast DNA sequencing via transverse electronic transport. Nano Lett. 2006;6(4):779-82.
[20] Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biol. 2007;8(1):R10.
[21] Quaiser A, Ochsenreiter T, Klenk HP, Kletzin A, Treusch AH, Meurer G, Eck J, Sensen CW, Schleper C. First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol. 2002;4(10):603-11.
[22] Yang ZhH, Xiao Y, Zeng GM, Xu ZhY, Liu YSh. Comparison of methods for total community DNA extraction and purification from compost. Appl Microbiol Biotechnol. 2007;74(4):918-25.
[23] Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. Bacteriol. 1996;178(3):591-9.
[24] Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007;17(3):377-86.
[25] Reva ON, Tummler B. Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformatics. 2004;5:90.
[26] Reva ON, Tummler B. Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. BMC Bioinformatics. 2005;6:251.
[27] Sandberg R, Winberg G, Branden CI, Kaske A, Ernberg I, C?ster J. Capturing whole-genome characteristics in short sequences using a na?ve Bayesian classifier. Genome Res. 2001;11(8):1404-9.
[28] He PA. The sieve ratio for characterization and similarity analysis of DNA sequences. Comb Chem High Throughput Screen. 2005;8(5):449-53.
[29] Teeling H, Meyerdierks A, Bauer M, Amann R, Glockner FO. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol. 2004;6(9):938-47.
[30] Williamson LL, Borlee BR, Schloss PD, Guan C, Allen HK, Handelsman J. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol. 2005;71(10):6335-44.
[31] 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(1):88-93.
[32] Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270(5235):467-70.
[33] Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol. 2000;66(6):2541-7.
[34] Wagner M, Nielsen PH, Loy A, Nielsen JL, Daims H. Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr Opin Biotechnol. 2006;17(1):83-91.
[35] Hatamoto M, Imachi H, Ohashi A, Harada H. Identification and cultivation of anaerobic, syntrophic long-chain fatty acid-degrading microbes from mesophilic and thermophilic methanogenic sludges. Appl Environ Microbiol. 2007;73(4):1332-40.
[36] Ariesyady HD, Ito T, Yoshiguchi K, Okabe S. Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge. Appl Microbiol Biotechnol. 2007;75(3):673-83.
[37] Whiteley AS, Thomson B, Lueders T, Manefield M. RNA stable-isotope probing. Nat Protoc. 2007;2(4):838-44.
[38] Bernard L, Mougel C, Maron PA, Nowak V, Leveque J, Henault C, Haichar FZ, Berge O, Marol C, Balesdent J, Gibiat F, Lemanceau P, Ranjard L. Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ Microbiol. 2007;9(3):752-64.
[39] Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Roslev P, Wagner M. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol. 2003;69(11):6875-87.
[40] Schmeisser C, Steele H, Streit WR. Metagenomics, biotechnology with non-culturable microbes. Appl Microbiol Biotechnol. 2007;75(5):955-62.
[41] Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 2005;6(8):229.
[42] Gabor EM, Alkema WB, Janssen DB. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol. 2004;6(9):879-86.
[43] Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Santos VA, Strompl C, Elborough K, Jarvis G, Neef A, Yakimov MM, Timmis KN, Golyshin PN. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ Microbiol. 2005;7(12):1996-2010.
[44] Rhee JK, Ahn DG, Kim YG, Oh JW. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl Environ Microbiol. 2005;71(2):817-25.
[45] Lopez-Cortes N, Reyes-Duarte D, Beloqui A, Polaina J, Ghazi I, Golyshina OV, Ballesteros A, Golyshin PN, Ferrer M. Catalytic role of conserved HQGE motif in the CE6 carbohydrate esterase family. FEBS Lett. 2007;581(24):4657-62.
[46] Richardson TH, Tan X, Frey G, Callen W, Cabell M, Lam D, Macomber J, Short JM, Robertson DE, Miller C. A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase. J Biol Chem. 2002;277(29):26501-7.
[47] Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR. Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol. 2003;69(10):6235-42.
[48] Yun J, Kang S, Park S, Yoon H, Kim MJ, Heu S, Ryu S. Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Appl Environ Microbiol. 2004;70(12):7229-35.
[49] Grant S, Sorokin DY, Grant WD, Jones BE, Heaphy S. A phylogenetic analysis of Wadi el Natrun soda lake cellulase enrichment cultures and identification of cellulase genes from these cultures. Extremophiles. 2004;8(5):421-9.
[50] Voget S, Steele HL, Streit WR. Characterization of a metagenome-derived halotolerant cellulase. J Biotechnol. 2006;126(1):26-36.
[51] Cottrell MT, Moore JA, Kirchman DL. Chitinases from uncultured marine microorganisms. Appl Environ Microbiol. 1999;65(6):2553-7.
[52] Hoster F, Schmitz JE, Daniel R. Enrichment of chitinolytic microorganisms: isolation and characterization of a chitinase exhibiting antifungal activity against phytopathogenic fungi from a novel Streptomyces strain. Appl Microbiol Biotechnol. 2005;66(4):434-42.
[53] Brennan Y, Callen WN, Christoffersen L, Dupree P, Goubet F, Healey S, Hern?ndez M, Keller M, Li K, Palackal N, Sittenfeld A, Tamayo G, Wells S, Hazlewood GP, Mathur EJ, Short JM, Robertson DE, Steer BA. Unusual microbial xylanases from insect guts. Appl Environ Microbiol. 2004;70(6):3609-17.
[54] Lee CC, Kibblewhite-Accinelli RE, Wagschal K, Robertson GH, Wong DW. Cloning and characterization of a cold-active xylanase enzyme from an environmental DNA library. Extremophiles. 2006;10(4):295-300.
[55] Ferrer M, Beloqui A, Golyshina OV, Plou FJ, Neef A, Chernikova TN, Fernandez-Arrojo L, Ghazi I, Ballesteros A, Elborough K, Timmis KN, Golyshin PN. Biochemical and structural features of a novel cyclodextrinase from cow rumen metagenome. Biotechnol J. 2007;2(2):207-13.
[56] Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355-9.
[57] Lim BL, Yeung P, Cheng C, Hill JE. Distribution and diversity of phytate-mineralizing bacteria. ISME J. 2007;1(4):321-30.
[58] Entcheva P, Liebl W, Johann A, Hartsch T, Streit WR. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl Environ Microbiol. 2001;67(1):89-99.
[59] Eschenfeldt WH, Stols L, Rosenbaum H, Khambatta ZS, Quaite-Randall E, Wu S, Kilgore DC, Trent JD, Donnelly MI. DNA from uncultured organisms as a source of 2,5-diketo-D-gluconic acid reductases. Appl Environ Microbiol. 2001;67(9):4206-14.
[60] DeSantis G, Zhu Z, Greenberg WA, Wong K, Chaplin J, Hanson SR, Farwell B, Nicholson LW, Rand CL, Weiner DP, Robertson DE, Burk MJ. An enzyme library approach to biocatalysis: development of nitrilases for enantioselective production of carboxylic acid derivatives. J Am Chem Soc. 2002;124(31):9024-5.
[61] Robertson DE, Chaplin JA, DeSantis G, Podar M, Madden M, Chi E, Richardson T, Milan A, Miller M, Weiner DP, Wong K, McQuaid J, Farwell B, Preston LA, Tan X, Snead MA, Keller M, Mathur E, Kretz PL, Burk MJ, Short JM. Exploring nitrilase sequence space for enantioselective catalysis. Appl Environ Microbiol. 2004;70(4):2429-36.
[62] Knietsch A, Bowien S, Whited G, Gottschalk G, Daniel R. Identification and characterization of coenzyme B12-dependent glycerol dehydratase- and diol dehydratase-encoding genes from metagenomic DNA libraries derived from enrichment cultures. Appl Environ Microbiol. 2003;69(6):3048-60.
[63] Beloqui A, Pita M, Polaina J, Martinez-Arias A, Golyshina OV, Zumarraga M, Yakimov MM, Garcia-Arellano H, Alcalde M, Fernandez VM, Elborough K, Andreu JM, Ballesteros A, Plou FJ, Timmis KN, Ferrer M, Golyshin PN. Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis, and phylogenetic relationships. J Biol Chem. 2006;281(32):22933-42.
[64] Gupta R, Beg QK, Lorenz P. Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol. 2002;59(1):15-32.
[65] Wang C, Meek DJ, Panchal P, Boruvka N, Archibald FS, Driscoll BT, Charles TC. Isolation of poly-3-hydroxybutyrate metabolism genes from complex microbial communities by phenotypic complementation of bacterial mutants. Appl Environ Microbiol. 2006;72(1):384-91.
[66] Brady SF, Chao CJ, Clardy J. Long-chain N-acyltyrosine synthases from environmental DNA. Appl Environ Microbiol. 2004;70(11):6865-70.
[67] Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304(5667):66-74.
[68] McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods. 2007;4(1):63-72.
[69] von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science. 2007;315(5815):1126-30.
[70] Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F. The marine viromes of four oceanic regions. PLoS Biol. 2006;4(11):e368.
[71] Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428(6978):37-43.
[72] Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC 2nd, Shah M, Hettich RL, Banfield JF. Community proteomics of a natural microbial biofilm. Science. 2005;308(5730):1915-20.
[73] Gans J, Wolinsky M, Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science. 2005;309(5739):1387-90.
[74] Daniel R. The metagenomics of soil. Nat Rev Microbiol. 2005;3(6):470-8.
[75] Nakatsu CH. Soil microbial community analysis using denaturing gradient gel electrophoresis. Soil Sci. Soc. Amer. J. 2007; 71(2):562–571.
[76] Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007;1(4):283-90.
[77] Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM. Comparative metagenomics of microbial communities. Science. 2005;308(5721):554-7.
[78] Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science. 2005;308(5728):1635-8.
[79] Okada M, Bothin C, Kanazawa K, Midtvedt T. Experimental study of the influence of intestinal flora on the healing of intestinal anastomoses. Br J Surg. 1999;86(7):961-5.
[80] Dymock D, Weightman AJ, Scully C, Wade WG. Molecular analysis of microflora associated with dentoalveolar abscesses. J Clin Microbiol. 1996;34(3):537-42.
[81] Kroes I, Lepp PW, Relman DA. Bacterial diversity within the human subgingival crevice. Proc Natl Acad Sci U S A. 1999;96(25):14547-52.
[82] Sakamoto M, Umeda M, Ishikawa I, Benno Y. Comparison of the oral bacterial flora in saliva from a healthy subject and two periodontitis patients by sequence analysis of 16S rDNA libraries. Microbiol Immunol. 2000;44(8):643-52.
[83] Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.
[84] Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4:41.
[85] Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol. 2007;9(11):2707-19.