Chapter 2.4.3 : Functional Metagenomics: Procedures and Progress

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Using metagenomic approaches to interrogate microbial communities is commonly based on sequencing the total DNA extracted from biomass. However, while this approach predominates in the literature, it does not provide an insight into the novel functions within a system and does not provide physical DNA for manipulation. In order to obtain novel functions from a microbial community, functional metagenomics was developed. This approach, which preceded the advent of large-scale sequence based metagenomics coupled with next generation sequencing, revolves around hosting and expressing heterologous DNA in a suitable surrogate host. Coupled with phenotypic screens functional metagenomics provides an alternative approach to obtaining functionally active genes from a microbial system, without the need to culture any organisms.

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3
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1. Herlemann DPR, Lundin D, Labrenz M, Jurgens K, Zheng Z, Aspeborg H, Andersson AF. 2013. Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class spartobacteria. mBio 4 : e00569-12.[PubMed][CrossRef]
2. 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 Y-H, Smith HO. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 : 66 74.[PubMed][CrossRef]
3. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform 9: 386.[CrossRef]
4. 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, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464 : 59 65.[PubMed][CrossRef]
5. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR, Peavy H, Pontzer C, Portnoy M, Sayre MH, Starke-Reed P, Zakhari S, Read J, Watson B, Guyer M. 2009. The NIH Human Microbiome Project. Genome Res 19 : 2317 2323.[PubMed][CrossRef]
6. Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S. 2014. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32 : 834 841.[PubMed][CrossRef]
7. Prakash T, Taylor TD. 2012. Functional assignment of metagenomic data: challenges and applications. Brief Bioinform 13 : 711 727.[PubMed][CrossRef]
8. Gilbert J, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides NC, Glöckner FO, Klenk H-P, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R. 2010. The Earth Microbiome Project. Meeting report of the 1st EMP meeting on sample selection and acquisition. Argonne National Laboratory, Chicago, IL, 6 October 2010, Vol. 3.
9. Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM. 2009. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J 4 : 279 285.[CrossRef]
10. Kotik M. 2009. Novel genes retrieved from environmental DNA by polymerase chain reaction: current genome-walking techniques for future metagenome applications. J Biotechnol 144 : 75 82.[CrossRef]
11. Uchiyama T, Miyazaki K. 2009. Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 20 : 616 622.[PubMed][CrossRef]
12. Morris LS, Evans J, Marchesi JR. 2012. A robust plate assay for detection of extracellular microbial protease activity in metagenomic screens and pure cultures. J Microbiol Meth 91 : 144 146.[CrossRef]
13. Brady SF. 2007. Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat Protocols 2 : 1297 1305.[PubMed][CrossRef]
14. Smith PB, Hancock GA, Rhoden DL. 1969. Improved medium for detecting deoxyribonuclease-producing bacteria. Appl Microbiol 18 : 991 993.[PubMed]
15. Henne A, Schmitz RA, Bömeke M, Gottschalk G, Daniel R. 2000. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl Environ Microbiol 66 : 3113 3116.[PubMed][CrossRef]
16. Culligan EP, Sleator RD, Marchesi JR, Hill C. 2012. Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome. ISME J 6 : 1916 1925.[PubMed][CrossRef]
17. Shuman HA, Silhavy TJ. 2003. The art and design of genetic screens: Escherichia coli. Nat Rev Genet 4 : 419 431.[PubMed][CrossRef]
18. Allen HK, Donato J, Wang HH, Cloud-Hansen KA, Davies J, Handelsman J. 2010. Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol 8 : 251 259.[PubMed][CrossRef]
19. Allen HK, Moe LA, Rodbumrer J, Gaarder A, Handelsman J. 2008. Functional metagenomics reveals diverse [beta]-lactamases in a remote Alaskan soil. ISME J 3 : 243 251.[PubMed][CrossRef]
20. Kim Y-J, Choi G-S, Kim S-B, Yoon G-S, Kim Y-S, Ryu Y-W. 2006. Screening and characterization of a novel esterase from a metagenomic library. Prot Expr Purif 45 : 315 323.[CrossRef]
21. Henke E, Bornscheuer UT. 2002. Fluorophoric assay for the high-throughput determination of amidase activity. Anal Chem 75 : 255 260.[CrossRef]
22. Williamson LL, Borlee BR, Schloss PD, Guan C, Allen HK, Handelsman J. 2005. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol 71 : 6335 6344.[PubMed][CrossRef]
23. Handelsman J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68 : 669 685.[PubMed][CrossRef]
24. Courtois S, Cappellano CM, Ball M, Francou F-X, Normand P, Helynck G, Martinez A, Kolvek SJ, Hopke J, Osburne MS, August PR, Nalin R, Guérineau M, Jeannin P, Simonet P, Pernodet J-L. 2003. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69 : 49 55.[PubMed][CrossRef]
25. Jones BV, Begley MI, Hill C, Gahan CGM, Marchesi JR. 2008. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci 105 : 13580 13585.[PubMed][CrossRef]
26. Ni J, Yan Q, Yu Y. 2013. How much metagenomic sequencing is enough to achieve a given goal? Sci Rep 3 : 1968.[PubMed]
27. Ekkers DM, Cretoiu MS, Kielak AM, Elsas JD. 2012. The great screen anomaly—a new frontier in product discovery through functional metagenomics. Appl Microbiol Biotechnol 93 : 1005 1020.[PubMed][CrossRef]
28. Bertrand HLN, Poly F, Van VT, Lombard N, Nalin R, Vogel TM, Simonet P. 2005. High molecular weight DNA recovery from soils prerequisite for biotechnological metagenomic library construction. J Microbiol Meth 62 : 1 11.[CrossRef]
29. Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P. 2005. Metagenomic gene discovery: past, present and future. Trends Biotechnol 23 : 321 329.[PubMed][CrossRef]
30. Salonen A, Nikkila J, Jalanka-Tuovinen J, Immonen O, Rajilic-Stojanovic M, Kekkonen RA, Palva A, de Vos WM. 2010. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Metho 81 : 127 134.[CrossRef]
31. Purohit MK, Singh SP. 2009. Assessment of various methods for extraction of metagenomic DNA from saline habitats of coastal Gujarat (India) to explore molecular diversity. Lett Appl Microbiol 49 : 338 344.[PubMed][CrossRef]
32. Liles MR, Williamson LL, Rodbumrer J, Torsvik V, Goodman RM, Handelsman J. 2008. Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms. Appl Environ Microbiol 74 : 3302 3305.[PubMed][CrossRef]
33. Liles M, Williamson L, Handelsman J, Goodman R., 2004. Section 3 update: isolation of high molecular weight genomic DNA from soil bacteria for genomic library construction, p. 2741 2751. In Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans AD, van Elsas JD (eds), Molecular Microbial Ecology Manual. Springer, Dordrecht.
34. Lämmle K, Zipper H, Breuer M, Hauer B, Buta C, Brunner H, Rupp S. 2007. Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. J Biotechnol 127 : 575 592.[PubMed][CrossRef]
35. Hu Y, Zhang G, Li A, Chen J, Ma L. 2008. Cloning and enzymatic characterization of a xylanase gene from a soil-derived metagenomic library with an efficient approach. Appl Microbiol Biotechnol 80 : 823 830.[PubMed][CrossRef]
36. Waschkowitz T, Rockstroh S, Daniel R. 2009. Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries. Appl Environ Microbiol 75 : 2506 2516.[PubMed][CrossRef]
37. Altenbuchner J, Viell P, Pelletier I. 1992. Positive selection vectors based on palindromic DNA sequences. Meth Enzymolo 216 : 457 466.[CrossRef]
38. Behura SK, Severson DW. 2013. Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes. Biol Rev 88 : 49 61.[PubMed][CrossRef]
39. Kudla G, Murray AW, Tollervey D, Plotkin JB. 2009. Coding-sequence determinants of gene expression in Escherichia coli. Science 324 : 255 258.[PubMed][CrossRef]
40. Angelov A, Mientus M, Liebl S, Liebl W. 2009. A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles. Syst Appl Microbiol 32 : 177 185.[PubMed][CrossRef]
41. 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 : 948 958.[PubMed][CrossRef]
42. Gabor EM, Alkema WBL, Janssen DB. 2004. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol 6 : 879 886.[PubMed][CrossRef]
43. Bernstein JR, Bulter T, Shen CR, Liao JC. 2007. Directed evolution of ribosomal protein S1 for enhanced translational efficiency of high GC Rhodopseudomonas palustris DNA in Escherichia coli. J Biol Chem 282 : 18929 18936.[PubMed][CrossRef]
44. Leggewie C, Henning H, Schmeisser C, Streit WR, Jaeger K-E. 2006. A novel transposon for functional expression of DNA libraries. J Biotechnol 123 : 281 287.[PubMed][CrossRef]
45. Dobrijevic D, Di Liberto G, Tanaka K, de Wouters T, Dervyn R, Boudebbouze S, Binesse J, Blottiere HM, Jamet A, Maguin E, van de Guchte M. 2013. High-throughput system for the presentation of secreted and surface-exposed proteins from Gram-positive bacteria in functional metagenomics studies. PLOS One 8 : e65956.[PubMed][CrossRef]
46. McMahon MD, Guan C, Handelsman J, Thomas MG. 2012. Metagenomic analysis of Streptomyces lividans reveals host-dependent functional expression. Appl Environ Microbiol 78 : 3622 3629.[PubMed][CrossRef]
47. Craig JW, Chang F-Y, Kim JH, Obiajulu SC, Brady SF. 2010. Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. Appl Environ Microbiol 76 : 1633 1641.[PubMed][CrossRef]
48. Rabausch U, Juergensen J, Ilmberger N, Böhnke S, Fischer S, Schubach B, Schulte M, Streit WR. 2013. Functional screening of metagenome and genome libraries for detection of novel flavonoid-modifying enzymes. Appl Environ Microbiol 79 : 4551 4563[PubMed][CrossRef]
49. Simon C, Daniel R. 2009. Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 85 : 265 276.[PubMed][CrossRef]
50. Simon C, Herath J, Rockstroh S, Daniel R. 2009. Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice. Appl Environ Microbiol 75 : 2964 2968.[PubMed][CrossRef]
51. Jones BV, Sun F, Marchesi JR. 2007. Using skimmed milk agar to functionally screen a gut metagenomic library for proteases may lead to false positives. Lett Appl Microbiol 45 : 418 420.[PubMed][CrossRef]
52. Uchiyama T, Abe T, Ikemura T, Watanabe K. 2005. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotech 23 : 88 93.[CrossRef]
53. Uchiyama T, Miyazaki K. 2010. Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes. Appl Environ Microbiol 76 : 7029 7035.[PubMed][CrossRef]
54. 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 : 2541 2547.[PubMed][CrossRef]
55. Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Doré JL, Henrissat B, Remaud-Siméon M, Monsan P, Potocki-Véronése G. 2013. Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS One 8 : e72766.[PubMed][CrossRef]
56. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74 : 5463 5467.[PubMed][CrossRef]
57. Wichmann F, Udikovic-Kolic N, Andrew S, Handelsman J. 2014. Diverse antibiotic resistance genes in dairy cow manure. mBio 5 : e01017-13.[PubMed][CrossRef]
58. Hall T. 2005. BioEdit. Biological sequence alignment editor for Win95. http://www.mbio.ncsu.edu/bioedit/bioedit.html
59. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 : 2725 2729[PubMed][CrossRef]
60. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. 2003. Database resources of the National Center for Biotechnology. Nucleic Acids Res 31 : 28 33.[PubMed][CrossRef]
61. Rawlings ND, Barrett AJ, Bateman A. 2012. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 40 : D343 D350.[PubMed][CrossRef]
62. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. 2013. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42 : D490 D495.[PubMed][CrossRef]
63. Fischer M, Pleiss J. 2003. The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Res 31 : 319 321.[PubMed][CrossRef]
64. Liu B, Pop M. 2009. ARDB—Antibiotic Resistance Genes Database. Nucleic Acids Res 37 : D443 D447.[PubMed][CrossRef]
65. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O'Brien JS, Pawlowski AC, Piddock LJV, Spanogiannopoulos P, Sutherland AD, Irene Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD. 2013. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57 : 3348 3357.[PubMed][CrossRef]
66. Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T. 2013. antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41 : W204 W212.[PubMed][CrossRef]
67. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R. 2011. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39 : W339 W346.[PubMed][CrossRef]
68. Schomburg D, Schomburg I. 2010. Enzyme databases. Meth Mol Biol 609 : 113 128.[CrossRef]
69. Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Dore J, Monsan P, Remaud-Simeon M, Potocki-Veronese G. 2010. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 20 : 1605 1612.[PubMed][CrossRef]
70. Owen JG, Robins KJ, Parachin NS, Ackerley DF. 2012. A functional screen for recovery of 4′-phosphopantetheinyl transferase and associated natural product biosynthesis genes from metagenome libraries. Environ Microbiol 14 : 1198 1209.[PubMed][CrossRef]
71. Pang H, Zhang P, Duan C-J, Mo X-C, Tang J-L, Feng J-X. 2009. Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase. Current Microbiology 58 : 404 408.[PubMed][CrossRef]
72. Nacke H, Will C, Herzog S, Nowka B, Engelhaupt M, Daniel R. 2011. Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories. FEMS Microbiol Ecol 78 : 188 201.[PubMed][CrossRef]
73. 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 1714.[PubMed][CrossRef]
74. Torres-Cortes G, Millan V, Ramirez-Saad HC, Nisa-Martinez R, Toro N, Martinez-Abarca F. 2011. Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples. Environ Microbiol 13 : 1101 1114.[PubMed][CrossRef]
75. Jones BV, Marchesi JR. 2007. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Meth 4 : 55 61.[CrossRef]
76. Rui He BW, Toshiyuki Wakimoto, Manyuan Wang, Liancai Zhu, and Ikuro Abe. 2013. Cyclodipeptides from metagenomic library of a japanese marine sponge. J Braz Chem Soc 24 : 1926 1932.
77. Lang KS, Anderson JM, Schwarz S, Williamson L, Handelsman J, Singer RS. 2010. Novel florfenicol and chloramphenicol resistance gene discovered in alaskan soil by using functional metagenomics. Appl Environ Microbiol 76 : 5321 5326.[PubMed][CrossRef]
78. Jeon JH, Kim JT, Lee HS, Kim S-J, Kang SG, Choi SH, Lee J-H. 2011. Novel lipolytic enzymes identified from metagenomic library of deep-sea sediment. Evid Based Complement Alternat Med doi: [PubMed]
79. Berlemont R, Delsaute M, Pipers D, D'Amico S, Feller G, Galleni M, Power P. 2009. Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples. ISME J 3 : 1070 1081.[PubMed][CrossRef]
80. Shao H, Xu L, Yan Y. 2013. Isolation and characterization of a thermostable esterase from a metagenomic library. J Ind Microbiol Biotechnol 40 : 1211 1222.[PubMed][CrossRef]
81. Biver S, Portetelle D, Vandenbol M. 2013. Characterization of a new oxidant-stable serine protease isolated by functional metagenomics. Springerplus 28 : 410. doi:10.1186/2193-1801-2-410.[CrossRef]
82. 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 16.[PubMed][CrossRef]
83. Lussier F-X, Chambenoit O, Côté A, Hupé J-F, Denis F, Juteau P, Beaudet R, Shareck F. 2010. Construction and functional screening of a metagenomic library using a T7 RNA polymerase-based expression cosmid vector. J Ind Microbiol Biotechnol 38 : 1321 1328.[PubMed][CrossRef]
84. Neveu J, Regeard C, DuBow M. 2011. Isolation and characterization of two serine proteases from metagenomic libraries of the Gobi and Death Valley deserts. Appl Microbiol Biotechnol 91 : 635 644.[PubMed][CrossRef]
85. Donato JJ, Moe LA, Converse BJ, Smart KD, Berklein EC, McManus PS, Handelsman J. 2010. Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins. Appl Environ Microbiol 76 : 4396 4401.[PubMed][CrossRef]
86. Yao J, Fan XJ, Lu Y, Liu YH. 2011. Isolation and Characterization of a Novel Tannase from a Metagenomic Library. J Agric Food Chem 59 : 3812 3818.[PubMed][CrossRef]


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Advantages and disadvantages of the two main types of metagenomic approaches

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3
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List of common screens used in functional metagenomics

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3
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List of screens used on a functional metagenomic fosmid library from the distal human gut and examples of hit rate

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3
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Recent (2010-present) successful functional metagenomic studies summarizing host organism(s) for library construction, types of genes targeted, diverse environments DNA was isolated from for metagenomic screening, type of vector used (with average metagenomic insert size), hit rate, and type of screening method implemented

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3

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