全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...

Metagenomics: An Application Based Perspective

DOI: 10.1155/2014/146030

Full-Text   Cite this paper   Add to My Lib

Abstract:

Metagenomics deals with the isolation of genetic material directly recovered from environmental samples. Metagenomics as an approach has emerged over the past two decades to elucidate a host of microbial communities inhabiting a specific niche with the goal of understanding their genetic diversity, population structure, and ecological role played by them. A number of new and novel molecules with significant functionalities and applications have been identified through this approach. In fact, many investigators are engaged in this field to unlock the untapped genetic resources with funding from governments sector. The sustainable economic future of modern industrialized societies requires the development of novel molecules, enzymes, processes, products, and applications. Metagenomics can also be applied to solve practical challenges in the field of medicine, agriculture, sustainability, and ecology. Metagenomics promises to provide new molecules and novel enzymes with diverse functions and enhanced features compared to the enzymes from the culturable microorganisms. Besides the application of metagenomics for unlocking novel biocatalysts from nature, it also has found applications in fields as diverse as bioremediation, personalized medicine, xenobiotic metabolism, and so forth. 1. Introduction The term metagenomics, the genomic analysis of a population of microorganisms, was coined by Handelsman et al. with a notion to analyse a collection of similar but not identical items, as in the statistical concept of meta-analysis [1]. The idea that the whole environmental microbiome can be explored and analysed together has revolutionized our understanding of the ecology around us. It has opened new horizons in the development of biotechnology based on the exploitation of uncultivated microbial species. The vast majority of microorganisms being unculturable [2], metagenomics has resulted in discoveries that remained hidden from the traditional culturing techniques. Though a multifaceted approach, the crux of applied metagenomics is to express recovered genes in a cultivable heterologous host. A booming area of biotechnology is the industrial use of microorganisms to produce antibiotics, enzymes, and other bioactive compounds. The demand for the commercial production of enzymes that are used in large-scale industrial processes is growing rapidly. The industrial applications of metagenomics include identification of novel biocatalysts, discovery of new antibiotics, personalized medicine, and bioremediation. In addition, biosurfactant producing bacteria have been

References

[1]  J. Handelsman, M. R. Rondon, S. F. Brady, J. Clardy, and R. M. Goodman, “Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products,” Chemistry and Biology, vol. 5, no. 10, pp. R245–R249, 1998.
[2]  V. Torsvik, J. Goksoyr, and F. L. Daae, “High diversity in DNA of soil bacteria,” Applied and Environmental Microbiology, vol. 56, no. 3, pp. 782–787, 1990.
[3]  J. A. Gilbert and C. L. Dupont, “Microbial metagenomics: beyond the genome,” Annual Review of Marine Science, vol. 3, pp. 347–371, 2011.
[4]  T. Nguyen, D. You, E. Kanaya, Y. Koga, and S. Kanaya, “Crystal structure of metagenome-derived LC9-RNase H1 with atypical DEDN active site motif,” The FEBS Letters, vol. 587, no. 9, pp. 1418–1423, 2013.
[5]  O. López-López, M. E. Cerdán, and M. I. Gonzalez-Siso, “New extremophilic lipases and esterases from metagenomics,” Current Protein and Peptide Science, vol. 15, pp. 445–455, 2014.
[6]  M. Schallmey, A. Ly, C. Wang et al., “Harvesting of novel polyhydroxyalkanaote (PHA) synthase encoding genes from a soil metagenome library using phenotypic screening,” FEMS Microbiology Letters, vol. 321, no. 2, pp. 150–156, 2011.
[7]  S. Cheema, M. Bassas-Galia, P. M. Sarma, B. Lal, and S. Arias, “Exploiting metagenomic diversity for novel polyhydroxyalkanoate synthases: production of a terpolymer poly(3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate) with a recombinant Pseudomonas putida strain,” Bioresource Technology, vol. 103, no. 1, pp. 322–328, 2012.
[8]  P. Lorenz, K. Liebeton, F. Niehaus, and J. Eck, “Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space,” Current Opinion in Biotechnology, vol. 13, no. 6, pp. 572–577, 2002.
[9]  P. D. Schloss and J. Handelsman, “Biotechnological prospects from metagenomics,” Current Opinion in Biotechnology, vol. 14, no. 3, pp. 303–310, 2003.
[10]  D. B. Wilson, “Cellulases and biofuels,” Current Opinion in Biotechnology, vol. 20, no. 3, pp. 295–299, 2009.
[11]  M. Hess, A. Sczyrba, R. Egan et al., “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen,” Science, vol. 331, no. 6016, pp. 463–467, 2011.
[12]  Y. Yeh, S. C. Chang, H. Kuo, C. Tong, S. Yu, and T. D. Ho, “A metagenomic approach for the identification and cloning of an endoglucanase from rice straw compost,” Gene, vol. 519, no. 2, pp. 360–366, 2013.
[13]  A. Bhat, S. Riyaz-Ul-Hassan, N. Ahmad, N. Srivastava, and S. Johri, “Isolation of cold-active, acidic endocellulase from Ladakh soil by functional metagenomics,” Extremophiles, vol. 17, no. 2, pp. 229–239, 2013.
[14]  H. Nacke, M. Engelhaupt, S. Brady, C. Fischer, J. Tautzt, and R. Daniel, “Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes,” Biotechnology Letters, vol. 34, no. 4, pp. 663–675, 2012.
[15]  T. M. Alvarez, J. H. Paiva, D. M. Ruiz et al., “Structure and function of a novel cellulase 5 from sugarcane soil metagenome,” PLoS ONE, vol. 8, no. 12, Article ID e83635, 2013.
[16]  C.-J. Duan, L. Xian, G.-C. Zhao et al., “Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens,” Journal of Applied Microbiology, vol. 107, no. 1, pp. 245–256, 2009.
[17]  S. Voget, H. L. Steele, and W. R. Streit, “Characterization of a metagenome-derived halotolerant cellulase,” Journal of Biotechnology, vol. 126, no. 1, pp. 26–36, 2006.
[18]  F. Ferrato, F. Carriere, L. Sarda, and R. Verger, “A critical reevaluation of the phenomenon of interfacial activation,” Methods in Enzymology, vol. 286, pp. 327–347, 1997.
[19]  K. Jaeger and T. Eggert, “Lipases for biotechnology,” Current Opinion in Biotechnology, vol. 13, no. 4, pp. 390–397, 2002.
[20]  P. K. Ghosh, R. K. Saxena, R. Gupta, R. P. Yadav, and S. Davidson, “Microbial lipases: production and applications,” Science progress, vol. 79, p. 2, 1996.
[21]  S. Nagarajan, “New tools for exploring old friends-microbial lipases,” Applied Biochemistry and Biotechnology, vol. 168, no. 5, pp. 1163–1196, 2012.
[22]  Q. Peng, X. Wang, M. Shang et al., “Isolation of a novel alkaline-stable lipase from a metagenomic library and its specific application for milkfatflavor production,” Microbial Cell Factories, vol. 13, no. 1, 2014.
[23]  M. Lee, C. Lee, T. Oh, J. K. Song, and J. Yoon, “Isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases,” Applied and Environmental Microbiology, vol. 72, no. 11, pp. 7406–7409, 2006.
[24]  F. H?rdeman and S. Sj?ling, “Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment,” FEMS Microbiology Ecology, vol. 59, no. 2, pp. 524–534, 2007.
[25]  J. Selvin, J. Kennedy, D. P. H. Lejon, G. S. Kiran, and A. D. W. Dobson, “Isolation identification and biochemical characterization of a novel halo-tolerant lipase from the metagenome of the marine sponge Haliclona simulans,” Microbial Cell Factories, vol. 11, article 72, 2012.
[26]  T. D. Ngo, B. H. Ryu, H. Ju et al., “Structural and functional analyses of a bacterial homologue of hormone-sensitive lipase from a metagenomic library,” Acta Crystallographica D: Biological Crystallography, vol. 69, part 9, pp. 1726–1737, 2013.
[27]  J. Fu, H.-K. S. Leiros, D. de Pascale, K. A. Johnson, H.-M. Blencke, and B. Landfald, “Functional and structural studies of a novel cold-adapted esterase from an Arctic intertidal metagenomic library,” Applied Microbiology and Biotechnology, vol. 97, no. 9, pp. 3965–3978, 2013.
[28]  J. Chow, F. Kovacic, Y. Dall Antonia et al., “The metagenome-derived enzymes LipS and LipT increase the diversity of known lipases,” PLoS ONE, vol. 7, no. 10, Article ID e47665, 2012.
[29]  A. Glogauer, V. P. Martini, H. Faoro et al., “Identification and characterization of a new true lipase isolated through metagenomic approach,” Microbial Cell Factories, vol. 10, article 54, 2011.
[30]  L. Chang, M. Ding, L. Bao, Y. Chen, J. Zhou, and H. Lu, “Characterization of a bifunctional xylanase/endoglucanase from yak rumen microorganisms,” Applied Microbiology and Biotechnology, vol. 90, no. 6, pp. 1933–1942, 2011.
[31]  F. Cheng, J. Sheng, R. Dong, Y. Men, L. Gan, and L. Shen, “Novel xylanase from a holstein cattle rumen metagenomic library and its application in xylooligosaccharide and ferulic acid production from wheat straw,” Journal of Agricultural and Food Chemistry, vol. 60, no. 51, pp. 12516–12524, 2012.
[32]  Y. S. Jeong, H. B. Na, S. K. Kim et al., “Characterization of Xyn10J, a novel family 10 xylanase from a compost metagenomic library,” Applied Biochemistry and Biotechnology, vol. 166, no. 5, pp. 1328–1339, 2012.
[33]  D. Verma, Y. Kawarabayasi, K. Miyazaki, and T. Satyanarayana, “Cloning, expression and characteristics of a novel alkalistable and thermostablexylanase encoding gene ( Mxyl ) retrieved from compost-soil metagenome,” PLoS ONE, vol. 8, no. 1, Article ID e52459, 2013.
[34]  X. Gong, R. J. Gruniniger, R. J. Forster, R. M. Teather, and T. A. McAllister, “Biochemical analysis of a highly specific, pH stable xylanase gene identified from a bovine rumen-derived metagenomic library,” Applied Microbiology and Biotechnology, vol. 97, no. 6, pp. 2423–2431, 2013.
[35]  E. Orhan, D. Omay, and Y. Güvenilir, “Partial purification and characterization of protease enzyme from Bacillus subtilis and Bacillus cereus,” Applied Biochemistry and Biotechnology A Enzyme Engineering and Biotechnology, vol. 121, no. 1–3, pp. 183–194, 2005.
[36]  S. Biver, D. Portetelle, and M. Vandenbol, “Characterization of a new oxidant-stable serine protease isolated by functional metagenomics,” SpringerPlus, vol. 2, article 410, 2013.
[37]  F. Niehaus, E. Gabor, S. Wieland, P. Siegert, K. H. Maurer, and J. Eck, “Enzymes for the laundry industries: tapping the vast metagenomic pool of alkaline proteases,” Microbial Biotechnology, vol. 4, no. 6, pp. 767–776, 2011.
[38]  T. J. Neveu, C. Regeard, and M. S. Dubow, “Isolation and characterization of two serine proteases from metagenomic libraries of the Gobi and Death Valley deserts,” Applied Microbiology and Biotechnology, vol. 91, no. 3, pp. 635–644, 2011.
[39]  P. L. Pushpam, T. Rajesh, and P. Gunasekaran, “Identification and characterization of alkaline serine protease from goat skin surface metagenome,” AMB Express, vol. 1, article 3, 2011.
[40]  R. Singh, S. Dhawan, K. Singh, and J. Kaur, “Cloning, expression and characterization of a metagenome derived thermoactive/thermostable pectinase,” Molecular Biology Reports, vol. 39, no. 8, pp. 8353–8361, 2012.
[41]  H. Wang, X. Li, Y. Ma, and J. Song, “Characterization and high-level expression of a metagenome-derived alkaline pectatelyase in recombinant Escherichia coli,” Process Biochemistry, vol. 49, pp. 69–76, 2013.
[42]  A. Bordbar, K. Omidiyan, and R. Hosseinzadeh, “Study on interaction of α-amylase from Bacillus subtilis with cetyl trimethylammonium bromide,” Colloids and Surfaces B: Biointerfaces, vol. 40, no. 1, pp. 67–71, 2005.
[43]  S. Sharma, F. G. Khan, and G. N. Qazi, “Molecular cloning and characterization of amylase from soil metagenomic library derived from Northwestern Himalayas,” Applied Microbiology and Biotechnology, vol. 86, no. 6, pp. 1821–1828, 2010.
[44]  J. Vidya, S. Swaroop, S. K. Singh, D. Alex, R. K. Sukumaran, and A. Pandey, “Isolation and characterization of a novel α-amylase from a metagenomic library of Western Ghats of Kerala, India,” Biologia, vol. 66, no. 6, pp. 939–944, 2011.
[45]  D. E. Gillespie, S. F. Brady, A. D. Bettermann et al., “Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA,” Applied and Environmental Microbiology, vol. 68, no. 9, pp. 4301–4306, 2002.
[46]  F. Chang and S. F. Brady, “Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 7, pp. 2478–2483, 2013.
[47]  H. K. Allen, L. A. Moe, J. Rodbumrer, A. Gaarder, and J. Handelsman, “Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil,” The ISME Journal, vol. 3, no. 2, pp. 243–251, 2009.
[48]  S. F. Brady, C. J. Chao, J. Handelsman, and J. Clardy, “Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA,” Organic Letters, vol. 3, no. 13, pp. 1981–1984, 2001.
[49]  Z. Feng, D. Chakraborty, S. B. Dewell, B. V. B. Reddy, and S. F. Brady, “Environmental DNA-encoded antibiotics fasamycins A and B inhibit FabF in type II fatty acid biosynthesis,” Journal of the American Chemical Society, vol. 134, no. 6, pp. 2981–2987, 2012.
[50]  G. Wang, E. Graziani, B. Waters et al., “Novel natural products from soil DNA libraries in a streptomycete host,” Organic Letters, vol. 2, no. 16, pp. 2401–2404, 2000.
[51]  H. K. Lim, E. J. Chung, J. Kim et al., “Characterization of a forest soil metagenome clone that confers indirubin and indigo production on Escherichia coli,” Applied and Environmental Microbiology, vol. 71, no. 12, pp. 7768–7777, 2005.
[52]  J. J. Banik and S. F. Brady, “Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules,” Current Opinion in Microbiology, vol. 13, no. 5, pp. 603–609, 2010.
[53]  L. L. Williamson, B. R. Borlee, P. D. Schloss, C. Guan, H. K. Allen, and J. Handelsman, “Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor,” Applied and Environmental Microbiology, vol. 71, no. 10, pp. 6335–6344, 2005.
[54]  Human Microbiome Project Consortium, “Structure, function and diversity of the healthy human microbiome,” Nature, vol. 486, pp. 207–214, 2012.
[55]  C. F. Maurice, H. J. Haiser, and P. J. Turnbaugh, “Xenobiotics shape the physiology and gene expression of the active human gut microbiome,” Cell, vol. 152, no. 1-2, pp. 39–50, 2013.
[56]  J. Kennedy, N. D. O'Leary, G. S. Kiran et al., “Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems,” Journal of Applied Microbiology, vol. 111, no. 4, pp. 787–799, 2011.
[57]  M. Pacwa-P?ociniczak, G. A. P?aza, Z. Piotrowska-Seget, and S. S. Cameotra, “Environmental applications of biosurfactants: recent advances,” International Journal of Molecular Sciences, vol. 12, no. 1, pp. 633–654, 2011.
[58]  N. G. K. Karanth, P. G. Deo, and N. K. Veenanadig, “Microbial production of biosurfactants and their importance,” Current Science, vol. 77, no. 1, pp. 116–126, 1999.
[59]  A. Y. Burch, B. K. Shimada, P. J. Browne, and S. E. Lindow, “Novel high-throughput detection method to assess bacterial surfactant production,” Applied and Environmental Microbiology, vol. 76, no. 16, pp. 5363–5372, 2010.
[60]  M. Morikawa, M. Ito, and T. Imanaka, “Isolation of a new surfactin producer Bacillus pumilus A-1, and cloning and nucleotide sequence of the regulator gene, psf-1,” Journal of Fermentation and Bioengineering, vol. 74, no. 5, pp. 255–261, 1992.
[61]  I. M. Banat, “The isolation of a thermophilic biosurfactant producing Bacillus sp.,” Biotechnology Letters, vol. 15, no. 6, pp. 591–594, 1993.
[62]  I. Siegmund and F. Wagner, “New method for detecting rhamnolipids excreted by Pseudomonas species during growth on mineral agar,” Biotechnology Techniques, vol. 5, no. 4, pp. 265–268, 1991.
[63]  T. Uchiyama and K. Watanabe, “Substrate-induced gene expression (SIGEX) screening of metagenome libraries,” Nature Protocols, vol. 3, no. 7, pp. 1202–1212, 2008.
[64]  D. Paul, G. Pandey, J. Pandey, and R. K. Jain, “Accessing microbial diversity for bioremediation and environmental restoration,” Trends in Biotechnology, vol. 23, no. 3, pp. 135–142, 2005.
[65]  M.-N. Xing, X.-Z. Zhang, and H. Huang, “Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis,” Biotechnology Advances, vol. 30, no. 4, pp. 920–929, 2012.
[66]  J. Neveu, C. Regeard, and M. S. Dubow, “Isolation and characterization of two serine proteases from metagenomic libraries of the Gobi and Death Valley deserts,” Applied Microbiology and Biotechnology, vol. 91, no. 3, pp. 635–644, 2011.

Full-Text

comments powered by Disqus

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133

WeChat 1538708413