Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry

  • Ramya Sree Boddu
  • K. DivakarEmail author


To meet the increase in demand for food and health-related products, there was a promptly growing trend in the food and pharmaceutical manufacturing industries in recent years. Microbial process plays main role in the manufacturing of food products for enhancement of taste, aroma, shelf- life and other probiotic applications. Microbes and microbial enzymes were used for manufacturing of pharmaceutical ingredients/products through biocatalysis and biotransformation and also for degradation of toxic chemical compounds in pharmaceutical industry waste. From a chosen environment, only small fraction of microbes can be cultured in the laboratory conditions, afore mentioned industries critically depends on these cultivable microbial communities to make use of microbes and microbial metabolites/enzymes. The microbial metagenomics, a culture independent technique has become a revolutionary tool for biotechnological applications, especially in food and pharmaceutical industries, which takes an advantage of identification of all the possible genomic information from chosen microbiome and to apply them for needs of an industry. In the recent years, metagenomics has been adopted to screen antimicrobial resistant genes, enzymes used for biotransformation of pharmaceutical ingredients and degradation of toxic chemicals from pharmaceutical industry wastes. In this book chapter, we discuss application of metagenomics on probiotics, detection and resistance developed by pathogens present in natural/ packed foods. Also we discuss various metagenome derived enzymes (nitrilases, β-glucosidase, lipases and esterases) applied for chiral synthesis of pharmaceutical ingredients and degradation of recalcitrant chemical compounds (nitroaromatic, Cyanide) from pharmaceutical industry and an overview on predicting novel antimicrobial resistance genes from uncultivable microbiome.


Antimicrobial resistance Enzymes Functional metagenomics Unculturable microbiome Probiotics 


  1. Allen HK, Moe LA, Rodbumrer J, Gaarder A, Handelsman J (2009) Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil. ISMEJ 3:243–251CrossRefGoogle Scholar
  2. Arbige MV, Freund PR, Silver SC, Zelko JT (1986) Novel lipase for cheddar cheese flavor development. Food Technol 40:91–96Google Scholar
  3. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J-M, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Bjørn NH, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, MetaHIT Consortium (additional members), Weissenbach J, Dusko ES, Bork P (2011) Enterotypes of the human gut microbiome. Nature 473:174–180CrossRefPubMedPubMedCentralGoogle Scholar
  4. Aw TG, Howe A, Rose JB (2014) Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater. J Virol Methods 210:15–21CrossRefPubMedGoogle Scholar
  5. Bartoloni A, Pallecchi L, Rodriguez H, Fernandez C, Mantella A, Bartalesi F, Strohmeyer M, Kristiansson C, Gotuzzo E, Paradisi F, Rossolini GM (2009) Antibiotic resistance in a very remote Amazonas community. Int J Antimicrob Agents 33:125–129CrossRefPubMedGoogle Scholar
  6. Benabbes L, Ollivier J, Schaeffer J, Parnaudeau S, Rhaissi H, Nourlil J, Le Guyader FS (2013) Norovirus and other human enteric viruses in moroccan shellfish. Food Environ Virol 5:35–40CrossRefPubMedGoogle Scholar
  7. Berdy J (2012) Thoughts and facts about antibiotics: where we are now and where we are heading. J Antibiot 65:385–395CrossRefPubMedGoogle Scholar
  8. Berman HF, Riley LW (2013) Identification of novel antimicrobial resistance genes from microbiota on retail spinach. BMC Microbiol 13:272CrossRefPubMedPubMedCentralGoogle Scholar
  9. Biver S, Steels S, Portetelle D, Vandenbol M (2013a) Bacillus subtilis as a tool for screening soil metagenomic libraries for antimicrobial activities. J Microbiol Biotechnol 23:850–855CrossRefPubMedGoogle Scholar
  10. Biver S, Portetelle D, Vandenbol M (2013b) Characterization of a new oxidant-stable serine protease isolated by functional metagenomics. Springerplus 2:410CrossRefPubMedPubMedCentralGoogle Scholar
  11. Bornscheuer UT (2002) Microbial carboxylesterases: classification, properties and application in biocatalysis. FEMS Microbiol Rev 26:73–81CrossRefPubMedGoogle Scholar
  12. Boyce COL (1986) Novo’s handbook of practical biotechnology. Novo Industri A/S, BagsvaerdGoogle Scholar
  13. Brady SF, Chao CJ, Clardy J (2004) Long-chain N-acyl tyrosine synthases from environmental DNA. Appl Environ Microbiol 70:6865–6870CrossRefPubMedPubMedCentralGoogle Scholar
  14. Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Dore J, Henrissat B, Remaud-Siméon M, Monsan P, Potocki-Véronèse G (2013) Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS ONE 8:e72766CrossRefPubMedPubMedCentralGoogle Scholar
  15. Cheng G, Hu Y, Yin Y, Yang X, Xiang C, Wang B, Chen Y, Yang F, Lei F, Wu N, Lu N, Li J, Chen Q, Li L, Zhu B (2012) Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion. FEMS Microbiol Lett 336:11–16CrossRefPubMedGoogle Scholar
  16. Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG (2015) The microbiome of uncontacted Amerindians. Sci Adv 1:e1500183CrossRefPubMedPubMedCentralGoogle Scholar
  17. Coughlan LM, Cotter PD, Hill C, Alvarez- Ordóñez A (2015) Biotechnological applications of functional metagenomics in the food and pharmaceutical industries. Front Microbiol 6(672)Google Scholar
  18. Culligan EP, Sleator RD, Marchesi JR, Hill C (2013) Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PLoS ONE 8(12):e82985CrossRefPubMedPubMedCentralGoogle Scholar
  19. Daniel R (2004) The soil metagenome – a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 15:199–204CrossRefPubMedGoogle Scholar
  20. DeSantis G, Zhu Z, Greenberg WA, Wong K, Chaplin J, Hanson SR, Farwell B, Nicholson LW, Rand CL, Weiner DP, Robertson DE, Burk MJ (2002) An enzyme library approach to biocatalysis: development of nitrilases for enantioselective production of carboxylic acid derivatives. J Am Chem Soc 124:9024–9025CrossRefPubMedGoogle Scholar
  21. Devirgiliis C, Zinno P, Stirpe M, Barile S, Perozzi G (2014) Functional screening of antibiotic resistance genes from a representative metagenomic library of food fermenting microbiota. Biomed Res Int 2014:290967CrossRefPubMedPubMedCentralGoogle Scholar
  22. Donato JJ, Moe LA, Converse BJ, Smart KD, Berklein FC, McManus P, Handelsman J (2010) Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins. Appl Environ Microbiol 76:4396–4401CrossRefPubMedPubMedCentralGoogle Scholar
  23. EFSA and ECDC (2013) European Food Safety Authority (EFSA), European Centre for Disease Prevention and Control (ECDC) The European union summary report on trends and sources of Zoonoses, Zoonotic agents and food-borne outbreaks in 2011. ESFA J 11(4):3129Google Scholar
  24. Elend C, Schmeisser C, Hoebenreich H, Steele HL, Streit WR (2007) Isolation and characterization of a metagenome-derived and cold-active lipase with high stereospecificity for (R)-ibuprofen esters. J Biotechnol 130:370–377CrossRefPubMedGoogle Scholar
  25. Erwin DP, Erickson IK, Delwiche ME, Colwell FS, Strap JL, Crawford RL (2005) Diversity of oxygenase genes frommethane- and ammonia-oxidizing bacteria in the Eastern Snake River Plain aquifer. Appl Environ Microbiol 71:2016–2025CrossRefPubMedPubMedCentralGoogle Scholar
  26. Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Yakimov MM, Martins dos Santos VAP, Timmis KN, Golyshin PN (2005a) Novel microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem Biol 12:895–904CrossRefPubMedGoogle Scholar
  27. Ferrer M, Martinez-Abarca F, Golyshin PN (2005b) Mining genomes and metagenomes. Curr Opin Biotechnol 16:588–593CrossRefPubMedGoogle Scholar
  28. Flint J, Duynhoven YV, Angulo FJ, DeLong SM, Braun P, Kirk M, Scallan E, Fitzgerald M, Adak GK, Sockett P, Ellis A, Hall G, Gargouri N, Walke H, Braam P (2005) Estimating the burden of acute gastroenteritis, foodborne disease, and pathogens commonly transmitted by food: an international review. Clin Infect Dis 41:698–704CrossRefPubMedGoogle Scholar
  29. Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, Dantas G (2012) The shared antibiotic resistome of soil bacteria and human pathogens. Science 337:1107–1111CrossRefPubMedPubMedCentralGoogle Scholar
  30. Fouhy F, Ogilvie LA, Jones BV, Ross RP, Ryan AC, Dempsey EM, Fitzgerald GF, Stanton C, Cotter PD (2014) Identification of aminoglycoside and beta-lactam resistance genes from within an infant gut functional metagenomic library. PLoSONE 9:e0108016CrossRefGoogle Scholar
  31. Gabor EM, de Vries EJ, Janssen DB (2004) 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 6:948–958CrossRefPubMedGoogle Scholar
  32. Gibson GR, Roberfroid MB (1995) Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 125:1401–1412PubMedGoogle Scholar
  33. Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM (2012) A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. PLoS Pathog 8:e1002924CrossRefPubMedPubMedCentralGoogle Scholar
  34. Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, Stryke D, Bouquet J, Somasekar S, Linnen JM, Dodd R, Mulembakani P, Schneider BS, Muyembe-Tamfum JJ, Stramer SL, Chiu CY (2015) Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med 7:99CrossRefPubMedPubMedCentralGoogle Scholar
  35. Guazzaroni ME, Morgante V, Mirete S, Gonzalez-Pastor JE (2013) Novel acid resistance genes from the metagenome of the Tinto River, an extremely acidic environment. Environ Microbiol 15:1088–1102CrossRefPubMedGoogle Scholar
  36. Gueimonde M, Collado MC (2012) Metagenomics and probiotics. Clin Microbiol Infect 4:32–34CrossRefGoogle Scholar
  37. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685CrossRefPubMedPubMedCentralGoogle Scholar
  38. Hawkey PM (2008) The growing burden of antimicrobial resistance. J Antimicrob Chemother 62:I1–I9CrossRefPubMedGoogle Scholar
  39. Hoessel R, Leclerc S, Endicott JA, Nobel MEM, Lawrie A, Tunnah P, Leost M, Damiens E, Marie D, Marko D, Niederberger E, Tang W, Eisenbrand G, Meijer L (1999) Indirubin, the active constituent of a Chinese anti leukaemia medicine, inhibits cyclin-dependent kinases. Nat Cell Biol 1:60–67CrossRefPubMedGoogle Scholar
  40. Jeon JH, Kim JT, Kim YJ, Kim HK, Lee HS, Kang SG, Kim SJ, Lee JH (2009) Cloning and characterization of a new cold-active lipase from a deep-sea sediment metagenome. Appl Microbiol Biotechnol 81:865–874CrossRefPubMedGoogle Scholar
  41. Joint F (2001) Who expert consultation on evaluation of health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria. Food and Agriculture Organization of the United Nations and the World Health Organization, CórdobaGoogle Scholar
  42. Kang CH, Oh KH, Lee MH, Oh TK, Kim BH, Yoon J (2011) A novel family VII esterase with industrial potential from compost metagenomic library. Microb Cell Fact 10:41CrossRefPubMedPubMedCentralGoogle Scholar
  43. Kilara A (1982) Enzymes and their uses in the processed apple industry: a review. Proc Biochem 17:35–41Google Scholar
  44. Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R (2003) Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli. J Mol Microbiol Biotechnol 5:46–56CrossRefPubMedGoogle Scholar
  45. Lawrence RH (1988) New applications of biotechnology in the food industry, biotechnology and the food supply: proceedings of a symposium, National Research Council (US) Commission on Life Sciences. National Academies Press (US), Washington, DC. Available from: Google Scholar
  46. Lee DG, Jeon JH, Jang MK, Kim NY, Lee JH, Lee JH, Kim SJ, Kim GD, Lee SH (2007) Screening and characterization of a novel fibrinolytic metalloprotease from a metagenomic library. Biotechnol Left 29:465–472CrossRefGoogle Scholar
  47. Liebeton K, Eck J (2004) Identification and expression in E. coli of novel nitrile hydratases from the metagenome. Eng Life Sci 4:557–562CrossRefGoogle Scholar
  48. Lim HK, Chung EJ, Kim JC, Choi GJ, Jang KS, Chung YR, Cho KY, Lee SW (2005) Characterization of a forest soil metagenome clone that confers indirubin and indigo production on Escherichia coli. Appl Environ Microbiol 71:7768–7777CrossRefPubMedPubMedCentralGoogle Scholar
  49. Lynch MF, Tauxe RV, Hedberg CW (2009) The growing burden of foodborne outbreaks due to contaminated fresh produce: risks and opportunities. Epidemiol Infect 137:307–315CrossRefPubMedGoogle Scholar
  50. Marko D, Schatzle S, Friedel A, Genzlinger A, Zankl H, Meijer L, Eisenbrand G (2001) Inhibition of cyclin- dependent kinase1 (CDK1) by indirubin derivatives in human tumour cells. Br J Cancer 84:283–289CrossRefPubMedPubMedCentralGoogle Scholar
  51. McGarvey KM, Queitsch K, Fields S (2012) Wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil DNA library. Appl Environ Microbiol 78:1708–1714CrossRefPubMedPubMedCentralGoogle Scholar
  52. Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P (2013) Metagenomics for pathogen detection in public health. Genom Med 5:81CrossRefGoogle Scholar
  53. Nieuwenhuijse DF, Koopmans MPG (2017) Metagenomic sequencing for surveillance of food and waterborne viral diseases. Front Microbiol 8:230CrossRefPubMedPubMedCentralGoogle Scholar
  54. Novakova J, Marian F (2013) Bioprospecting microbial metagenome for natural products. Biol Sect Cell Mol Biol 68:1079–1086Google Scholar
  55. Ogino H, Otsubo T, Ishikawa H (2008) Screening, purification, and characterization of a leather- degrading protease. Biochem Eng J 38:234–240CrossRefGoogle Scholar
  56. Ouyang LM, Liu JY, Qiao M, Xu JH (2013) Isolation and biochemical characterization of two novel metagenome-derived esterases. Appl Biochem Biotechnol 169:15–28CrossRefPubMedGoogle Scholar
  57. Pace HC, Brenner C (2001) The nitrilase superfamily: classification, structure and function. Genome Biol 2(1.): reviews):0001.1–0001.9CrossRefGoogle Scholar
  58. Pallecchi L, Bartoloni A, Paradisi F, Rossolini GM (2008) Antibiotic resistance in the absence of antimicrobial use: mechanisms and implications. Expert Rev Anti Infect Ther 6:725–732CrossRefPubMedGoogle Scholar
  59. Panda T, Gowrishankar BS (2005) Production and applications of esterases. Appl Microbiol Biotechnol 67:160–169CrossRefPubMedGoogle Scholar
  60. Patro JN, Ramachandran P, Barnaba T, Mammel MK, Lewis JL, Elkins CA (2016) Culture independent metagenomic surveillance of commercially available probiotics with high throughput next-generation sequencing. mSphere 1(2):e00057-16CrossRefPubMedPubMedCentralGoogle Scholar
  61. Peng Q, Wang X, Shang M, Huang J, Guan G, Li Y, Shi B (2014) Isolation of a novel alkaline-stable lipase from a metagenomic library and its specific application for milk fat flavour production. Microb Cell Fact 13:1CrossRefPubMedPubMedCentralGoogle Scholar
  62. Podar M, Eads J, Richardson TH (2005) Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study. BMC Evol Biol 5:42CrossRefPubMedPubMedCentralGoogle Scholar
  63. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto J-M, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65CrossRefPubMedPubMedCentralGoogle Scholar
  64. Rhee JK, Ahn DG, Kim YG, Oh JW (2005) New thermophilic and thermostable esterase with sequence similarity to the hormone- sensitive lipase family, cloned from a metagenomic library. Appl Environ Microbiol 71:817–825CrossRefPubMedPubMedCentralGoogle Scholar
  65. Rinkoo DG, Rakesh S (2011) Metagenomics for environmental and industrial microbiology. Sci Cult 77:1–2Google Scholar
  66. Robertson DE, Chaplin JA, DeSaritis 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 M, Keller M, Mathur E, Kretz PL, Burk MJ, Short JM (2004) Exploring nitrilase sequence space for enantioselective catalysis. Appl Environ Microbiol 70:2429–2436CrossRefPubMedPubMedCentralGoogle Scholar
  67. Roh C, Villatte F (2008) Isolation of a low-temperature adapted lipolytic enzyme from uncultivated micro-organism. J Appl Microbiol 105:116–123CrossRefPubMedGoogle Scholar
  68. 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 (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541CrossRefPubMedPubMedCentralGoogle Scholar
  69. Salminen S, Nurmi J, Gueimonde M (2005) The genomics of probiotic intestinal microorganisms. Genome Biol 6:225CrossRefPubMedPubMedCentralGoogle Scholar
  70. Sardi SI, Somasekar S, Naccache SN, Bandeira AC, Tauro LB, Campos GS et al (2016) Coinfections of Zika and Chikungunya viruses in Bahia, Brazil, identified by metagenomic next-generation sequencing. J Clin Microbiol 54:2348–2353CrossRefPubMedPubMedCentralGoogle Scholar
  71. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM (2011) Foodborne illness acquired in the United States–major pathogens. Emerg Infect Dis 17:7–15CrossRefPubMedPubMedCentralGoogle Scholar
  72. Scharff RL (2012) Economic burden from health losses due to foodborne illness in the United States. J Food Prot 75:123–131CrossRefPubMedGoogle Scholar
  73. Shen D, Xu JH, Wu HY, Liu YY (2002) Significantly improved esterase activity of Trichosporon brassicae cells for ketoprofen resolution by 2-propanol treatment. J Mol Catal BEnzym 18:219–224CrossRefGoogle Scholar
  74. Smits S, Zijlstra E, Hellemond J, Schapendonk C, Bodewes R, Schürch A, Haagmans B, Osterhaus A (2013) Novel Cyclovirus in human cerebrospinal fluid, Malawi, 2010–2011. Emerg Infect Dis 19(9):1511–1513CrossRefPubMedCentralGoogle Scholar
  75. Solbak AI, Richardson TH, McCann RT, Kline KA, Bartnek F, Tomlinson G, Tan X, Parra-Gessert L, Frey GJ, Podar M et al (2005) Discovery of pectin-degrading enzymes and directed evolution of a novel pectate lyase for processing cotton fabric. J Biol Chem 280:9431–9438CrossRefPubMedGoogle Scholar
  76. Sommer MOA, Dantas G, Church GM (2009) Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325:1128–1131CrossRefPubMedPubMedCentralGoogle Scholar
  77. Song JS, Jeon JH, Lee JH, Jeong SH, Jeong BC, Kim SJ, Lee JH, Lee SH (2005) Molecular characterization of TEM-type b-lactamases identified in cold-seep sediments of Edison Seamount (south of Lihir Island, Papua New Guinea). J Microbiol 43:172–178PubMedGoogle Scholar
  78. Streit WR, Schmitz RA (2004) Metagenomics – the key to the uncultured microbes. Curr Opin Microbiol 7:492–498CrossRefPubMedGoogle Scholar
  79. Su JQ, Wei B, Xu CY, Qiao M, Zhu YG (2014) Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China. Environ Int 65:9–15CrossRefPubMedGoogle Scholar
  80. Tao W, Lee MH, Wu J, Kim NH, Kim JC, Chung E et al (2012) Inactivation of chloramphenicol and florfenicol by a novel chloramphenicol hydrolase. Appl Environ Microbiol 78:6295–6301CrossRefPubMedPubMedCentralGoogle Scholar
  81. Torsten T, Jack G, Folker M (2012) Metagenomics – a guide from sampling to data analysis. Microb Inf Exp 2:3CrossRefGoogle Scholar
  82. Uchiyama T, Abe T, Ikemura T, Watanabe K (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23:88–93CrossRefPubMedGoogle Scholar
  83. Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger K-E, Streit WR (2003) Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol 69:6235–6242CrossRefPubMedPubMedCentralGoogle Scholar
  84. Walter J, Mangold M, Tannock GW (2005) Construction, analysis, and b-glucanase screening of a bacterial artificial chromosome library from the large-bowel microbiota of mice. Appl Environ Microbiol 71:2347–2354CrossRefPubMedPubMedCentralGoogle Scholar
  85. Wendel AM, Johnson DH, Sharapov U, Grant J, Archer JR, Monson T, Koschmann C, Davis JP (2009) Multistate Outbreak of Escherichia coli O157: H7 Infection associated with consumption of packaged spinach, August–September 2006: the Wisconsin investigation. Clin Infect Dis 48:1079–1086CrossRefPubMedGoogle Scholar
  86. Wong DWS (2010) Wong DWS (2010) Applications of metagenomics for industrial bioproducts. In: Marco D (ed) Metagenomics: theory, methods and applications. Caister Academic Press, Norfolk, pp 141–158. ISBN:978-1-904455-54-7Google Scholar
  87. Xu B, Zhi N, Hu G, Wan Z, Zheng X, Liu X, Wong S, Kajigaya S, Zhao K, Mao Q, Young NS (2013) Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing. Proc Natl Acad Sci USA 110:10264–10269CrossRefPubMedGoogle Scholar
  88. Yang X, Noyes NR, Doster E, Martin JN, Linke LM, Magnuson RJ, Yang H, Geornaras I, Woerner DR, Jones KL, Ruiz J, Boucher C, Morley PS, Belk KE (2016) Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within the microbiome of the beef production chain. Appl Environ Microbiol 82:2433–2443CrossRefPubMedPubMedCentralGoogle Scholar
  89. Yun J, Kang S, Park S, Yoon H, Kim MJ, Heu S, Ryu S (2004) Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Appl Environ Microbiol 70:7229–7235CrossRefPubMedPubMedCentralGoogle Scholar

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© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Department of BiotechnologyNational Institute of TechnologyWarangalIndia

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