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Volumn 25, Issue 6, 2009, Pages 945-954

Metagenomics as a new technological tool to gain scientific knowledge

Author keywords

Metagenomics; Microbial diversity; Systems microbiology

Indexed keywords

DNA SEQUENCING; ENCODED PROTEINS; EXPERIMENTAL TESTING; GENOMICS; METAGENOMES; METAGENOMICS; MICROBIAL COMMUNITIES; MICROBIAL DIVERSITY; NEW TOOLS; SCIENTIFIC KNOWLEDGE; SYSTEMS MICROBIOLOGY; TECHNOLOGICAL TOOLS;

EID: 67349122818     PISSN: 09593993     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11274-009-9971-z     Document Type: Article
Times cited : (28)

References (70)
  • 5
    • 34547347640 scopus 로고    scopus 로고
    • Functional metaproteome analysis of protein extracts from contaminated soil and groundwater
    • 10.1038/ismej.2007.39
    • D Benndorf GU Balcke H Harms M von Bergen 2007 Functional metaproteome analysis of protein extracts from contaminated soil and groundwater ISME J 3 224 234 10.1038/ismej.2007.39
    • (2007) ISME J , vol.3 , pp. 224-234
    • Benndorf, D.1    Balcke, G.U.2    Harms, H.3    Von Bergen, M.4
  • 6
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • 10.1016/j.gde.2006.10.009
    • DR Bentley 2006 Whole-genome re-sequencing Curr Opin Genet Dev 16 545 552 10.1016/j.gde.2006.10.009
    • (2006) Curr Opin Genet Dev , vol.16 , pp. 545-552
    • Bentley, D.R.1
  • 7
    • 48749117805 scopus 로고    scopus 로고
    • Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment
    • 10.1073/pnas.0709942105
    • JF Biddle S Fitz-Gibbon SC Schuster JE Brenchley CH House 2008 Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment Proc Natl Acad Sci USA 105 10583 10588 10.1073/pnas.0709942105
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 10583-10588
    • Biddle, J.F.1    Fitz-Gibbon, S.2    Schuster, S.C.3    Brenchley, J.E.4    House, C.H.5
  • 9
    • 33750705293 scopus 로고    scopus 로고
    • Integration of metabolome data with metabolic networks reveals reporter reactions
    • 10.1038/msb4100085
    • T Cakir KR Patil Z Onsan KO Ulgen B Kirdar J Nielsen 2006 Integration of metabolome data with metabolic networks reveals reporter reactions Mol Syst Biol 2 50 10.1038/msb4100085
    • (2006) Mol Syst Biol , vol.2 , pp. 50
    • Cakir, T.1    Patil, K.R.2    Onsan, Z.3    Ulgen, K.O.4    Kirdar, B.5    Nielsen, J.6
  • 10
    • 38649143159 scopus 로고    scopus 로고
    • Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing
    • 10.1155/2008/513701
    • CK Chan AL Hsu SL Tang SK Halgamuge 2008 Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing J Biomed Biotechnol 2008 513701 10.1155/2008/513701
    • (2008) J Biomed Biotechnol , vol.2008 , pp. 513701
    • Chan, C.K.1    Hsu, A.L.2    Tang, S.L.3    Halgamuge, S.K.4
  • 11
    • 33746921634 scopus 로고    scopus 로고
    • The personal genome project
    • JM Church 2005 The personal genome project Mol Syst Biol 1 20050030
    • (2005) Mol Syst Biol , vol.1 , pp. 20050030
    • Church, J.M.1
  • 13
    • 19144362371 scopus 로고    scopus 로고
    • Microbial community genomics in the ocean
    • 10.1038/nrmicro1158
    • EF DeLong 2005 Microbial community genomics in the ocean Nat Rev Microbiol 3 459 469 10.1038/nrmicro1158
    • (2005) Nat Rev Microbiol , vol.3 , pp. 459-469
    • Delong, E.F.1
  • 14
    • 33646244299 scopus 로고    scopus 로고
    • Archaeal mysteries of the deep revealed
    • 10.1073/pnas.0602079103
    • EF DeLong 2006 Archaeal mysteries of the deep revealed Proc Natl Acad Sci USA 103 6417 6418 10.1073/pnas.0602079103
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 6417-6418
    • Delong, E.F.1
  • 18
    • 33947221422 scopus 로고    scopus 로고
    • Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes
    • 10.1371/journal.pbio.0050082
    • JA Eisen 2007 Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes PLoS Biol 5 e82 10.1371/journal.pbio.0050082
    • (2007) PLoS Biol , vol.5 , pp. 82
    • Eisen, J.A.1
  • 19
    • 40849126953 scopus 로고    scopus 로고
    • Integrating global gene expression analysis and genetics
    • 10.1016/S0065-2660(07)00420-8
    • CR Farber AJ Lusis 2008 Integrating global gene expression analysis and genetics Adv Genet 60 571 601 10.1016/S0065-2660(07)00420-8
    • (2008) Adv Genet , vol.60 , pp. 571-601
    • Farber, C.R.1    Lusis, A.J.2
  • 22
    • 55249114699 scopus 로고    scopus 로고
    • Metagenomics for mining new genetic resources of microbial communities
    • 10.1159/000142898
    • M Ferrer A Beloqui KN Timmis PN Golyshin 2008 Metagenomics for mining new genetic resources of microbial communities J Mol Microbiol Biotechnol 16 109 123 10.1159/000142898
    • (2008) J Mol Microbiol Biotechnol , vol.16 , pp. 109-123
    • Ferrer, M.1    Beloqui, A.2    Timmis, K.N.3    Golyshin, P.N.4
  • 28
    • 42149162147 scopus 로고    scopus 로고
    • The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology
    • 10.1039/b717118h
    • PF Hallin TT Binnewies DW Ussery 2008 The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology Mol Biosyst 5 363 371 10.1039/b717118h
    • (2008) Mol Biosyst , vol.5 , pp. 363-371
    • Hallin, P.F.1    Binnewies, T.T.2    Ussery, D.W.3
  • 29
    • 10344227692 scopus 로고    scopus 로고
    • Metagenomics: Application of genomics to uncultured microorganisms
    • DOI 10.1128/MMBR.68.4.669-685.2004
    • J Handelsman 2004 Metagenomics: application of genomics to uncultured microorganisms Mol Biol Rep 68 669 685 (Pubitemid 39628532)
    • (2004) Microbiology and Molecular Biology Reviews , vol.68 , Issue.4 , pp. 669-685
    • Handelsman, J.1
  • 30
    • 43249100663 scopus 로고    scopus 로고
    • Metagenomics is not enough
    • 10.1089/dna.2008.1503
    • J Handelsman 2008 Metagenomics is not enough DNA Cell Biol 27 219 221 10.1089/dna.2008.1503
    • (2008) DNA Cell Biol , vol.27 , pp. 219-221
    • Handelsman, J.1
  • 31
    • 0032192790 scopus 로고    scopus 로고
    • Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products
    • J Handelsman MR Rondon SF Brady J Clardy RM Goodman 1998 Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products Chem Biol 5 245 249 10.1016/S1074-5521(98)90108-9 (Pubitemid 29000111)
    • (1998) Chemistry and Biology , vol.5 , Issue.10
    • Handelsman, J.1    Rondon, M.R.2    Brady, S.F.3    Clardy, J.4    Goodman, R.M.5
  • 32
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • 10.1101/gr.5969107
    • DH Huson AF Auch J Qi SC Schuster 2007 MEGAN analysis of metagenomic data Genome Res 3 377 386 10.1101/gr.5969107
    • (2007) Genome Res , vol.3 , pp. 377-386
    • Huson, D.H.1    Auch, A.F.2    Qi, J.3    Schuster, S.C.4
  • 34
    • 45849153461 scopus 로고    scopus 로고
    • Genomic sequencing of single microbial cells from environmental samples
    • 10.1016/j.mib.2008.05.006
    • T Ishoey T Woyke R Stepanauskas M Novotny RS Lasken 2008 Genomic sequencing of single microbial cells from environmental samples Curr Opin Microbiol 11 198 204 10.1016/j.mib.2008.05.006
    • (2008) Curr Opin Microbiol , vol.11 , pp. 198-204
    • Ishoey, T.1    Woyke, T.2    Stepanauskas, R.3    Novotny, M.4    Lasken, R.S.5
  • 35
    • 33749410295 scopus 로고    scopus 로고
    • Inference of population genetic parameters in metagenomics: A clean look at messy data
    • 10.1101/gr.5431206
    • PLF Johnson M Slatkin 2006 Inference of population genetic parameters in metagenomics: a clean look at messy data Genome Res 16 1320 1327 10.1101/gr.5431206
    • (2006) Genome Res , vol.16 , pp. 1320-1327
    • Johnson, P.L.F.1    Slatkin, M.2
  • 38
    • 35748983784 scopus 로고    scopus 로고
    • Single-cell genomic sequencing using multiple displacement amplification
    • 10.1016/j.mib.2007.08.005
    • RS Lasken 2007 Single-cell genomic sequencing using multiple displacement amplification Curr Opin Microbiol 10 510 516 10.1016/j.mib.2007.08.005
    • (2007) Curr Opin Microbiol , vol.10 , pp. 510-516
    • Lasken, R.S.1
  • 40
    • 38549144166 scopus 로고    scopus 로고
    • The genomes on line database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata
    • 10.1093/nar/gkm884
    • K Liolios K Mavromatis N Tavernarakis NC Kyrpides 2008 The genomes on line database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata Nucleic Acids Res 36 D475 D479 10.1093/nar/gkm884
    • (2008) Nucleic Acids Res , vol.36
    • Liolios, K.1    Mavromatis, K.2    Tavernarakis, N.3    Kyrpides, N.C.4
  • 43
    • 44849128805 scopus 로고    scopus 로고
    • Species divergence and the measurement of microbial diversity
    • 10.1111/j.1574-6976.2008.00111.x
    • CA Lozupone R Knight 2008 Species divergence and the measurement of microbial diversity FEMS Microbiol Rev 32 557 578 10.1111/j.1574-6976.2008. 00111.x
    • (2008) FEMS Microbiol Rev , vol.32 , pp. 557-578
    • Lozupone, C.A.1    Knight, R.2
  • 45
    • 20044362752 scopus 로고    scopus 로고
    • Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes
    • NISC Comparative Sequencing Program. 10.1073/pnas.0408539102
    • EH Margulies NISC Comparative Sequencing Program VV Maduro PJ Thomas JP Tomkins CT Amemiya M Luo ED Green 2005 Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes Proc Natl Acad Sci USA 102 3354 3359 10.1073/pnas.0408539102
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 3354-3359
    • Margulies, E.H.1    Maduro, V.V.2    Thomas, P.J.3    Tomkins, J.P.4    Amemiya, C.T.5    Luo, M.6    Green, E.D.7
  • 46
    • 35748959318 scopus 로고    scopus 로고
    • What's in the mix: phylogenetic classification of metagenome sequence samples
    • DOI 10.1016/j.mib.2007.08.004, PII S136952740700118X, Antimicrobials/Genomics
    • AC McHardy I Rigoutsos 2007 What's in the mix: phylogenetic classification of metagenome sequence samples Curr Opin Microbiol 10 449 503 (Pubitemid 350052685)
    • (2007) Current Opinion in Microbiology , vol.10 , Issue.5 , pp. 499-503
    • McHardy, A.C.1    Rigoutsos, I.2
  • 47
    • 33750976398 scopus 로고    scopus 로고
    • MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences
    • 10.1093/nar/gkl723
    • H Noguchi J Park T Takagi 2006 MetaGene: prokaryotic gene finding from environmental genome shotgun sequences Nucleic Acids Res 34 5623 5630 10.1093/nar/gkl723
    • (2006) Nucleic Acids Res , vol.34 , pp. 5623-5630
    • Noguchi, H.1    Park, J.2    Takagi, T.3
  • 48
    • 33746914768 scopus 로고    scopus 로고
    • Evolution of enzymatic activity in the tautomerase superfamily: Mechanistic and structural consequences of the L8R mutation in 4-oxalocrotonate tautomerase
    • 10.1021/bi0600603
    • GJ Poelarends JJ Almrud H Serrano JE Darty WH Johnson Jr ML Hackert CP Whitman 2006 Evolution of enzymatic activity in the tautomerase superfamily: mechanistic and structural consequences of the L8R mutation in 4-oxalocrotonate tautomerase Biochemistry 45 7700 7708 10.1021/bi0600603
    • (2006) Biochemistry , vol.45 , pp. 7700-7708
    • Poelarends, G.J.1    Almrud, J.J.2    Serrano, H.3    Darty, J.E.4    Johnson Jr, W.H.5    Hackert, M.L.6    Whitman, C.P.7
  • 49
    • 49649089054 scopus 로고    scopus 로고
    • Molecular eco-systems biology: Towards an understanding of community function
    • 10.1038/nrmicro1935
    • J Raes P Bork 2008 Molecular eco-systems biology: towards an understanding of community function Nat Rev Microbiol 6 693 699 10.1038/nrmicro1935
    • (2008) Nat Rev Microbiol , vol.6 , pp. 693-699
    • Raes, J.1    Bork, P.2
  • 50
    • 35748976529 scopus 로고    scopus 로고
    • Get the most out of your metagenome: Computational analysis of environmental sequence data
    • 10.1016/j.mib.2007.09.001
    • J Raes KU Foerstner P Bork 2007 Get the most out of your metagenome: computational analysis of environmental sequence data Curr Opin Microbiol 10 490 498 10.1016/j.mib.2007.09.001
    • (2007) Curr Opin Microbiol , vol.10 , pp. 490-498
    • Raes, J.1    Foerstner, K.U.2    Bork, P.3
  • 51
    • 4344587758 scopus 로고    scopus 로고
    • Uncultured soil bacteria are a reservoir of new antibiotic resistance genes
    • 10.1111/j.1462-2920.2004.00664.x
    • CS Riesenfeld RM Goodman J Handelsman 2004 Uncultured soil bacteria are a reservoir of new antibiotic resistance genes Environ Microbiol 6 981 989 10.1111/j.1462-2920.2004.00664.x
    • (2004) Environ Microbiol , vol.6 , pp. 981-989
    • Riesenfeld, C.S.1    Goodman, R.M.2    Handelsman, J.3
  • 52
    • 33947238287 scopus 로고    scopus 로고
    • The Sorcerer II global ocean sampling expedition: Northwest. Atlantic through eastern tropical Pacific
    • 10.1371/journal.pbio.0050077
    • DB Rusch AL Halpern G Sutton KB Heidelberg S Williamson S Yooseph 2007 The Sorcerer II global ocean sampling expedition: northwest. Atlantic through eastern tropical Pacific PLoS Biol 5 398 431 10.1371/journal.pbio.0050077
    • (2007) PLoS Biol , vol.5 , pp. 398-431
    • Rusch, D.B.1    Halpern, A.L.2    Sutton, G.3    Heidelberg, K.B.4    Williamson, S.5    Yooseph, S.6
  • 53
    • 33846061120 scopus 로고    scopus 로고
    • 13C-based flux analysis
    • 10.1038/msb4100109
    • 13C-based flux analysis Mol Syst Biol 2 62 10.1038/msb4100109
    • (2006) Mol Syst Biol , vol.2 , pp. 62
    • Sauer, U.1
  • 54
    • 33746639717 scopus 로고    scopus 로고
    • Toward a census of bacteria in soil
    • 10.1371/journal.pcbi.0020092
    • PD Schloss J Handelsman 2006 Toward a census of bacteria in soil PLOS Comput Biol 7 e92 10.1371/journal.pcbi.0020092
    • (2006) PLOS Comput Biol , vol.7 , pp. 92
    • Schloss, P.D.1    Handelsman, J.2
  • 55
    • 39049092823 scopus 로고    scopus 로고
    • A statistical toolbox for metagenomics: Assessing functional diversity in microbial communities
    • 10.1186/1471-2105-9-34
    • PD Schloss JA Handelsman 2008 A statistical toolbox for metagenomics: assessing functional diversity in microbial communities BMC Bioinformatics 9 34 10.1186/1471-2105-9-34
    • (2008) BMC Bioinformatics , vol.9 , pp. 34
    • Schloss, P.D.1    Handelsman, J.A.2
  • 56
    • 34250639490 scopus 로고    scopus 로고
    • Metagenomics, biotechnology with non-culturable microbes
    • 10.1007/s00253-007-0945-5
    • C Schmeisser H Steele WR Streit 2007 Metagenomics, biotechnology with non-culturable microbes Appl Microbiol Biotechnol 75 955 962 10.1007/s00253-007-0945-5
    • (2007) Appl Microbiol Biotechnol , vol.75 , pp. 955-962
    • Schmeisser, C.1    Steele, H.2    Streit, W.R.3
  • 57
    • 1942499454 scopus 로고    scopus 로고
    • Advanced sequencing technologies: Methods and goals
    • 10.1038/nrg1325
    • J Shendure RD Mitra C Varma GM Church 2004 Advanced sequencing technologies: methods and goals Nat Rev Genet 5 335 344 10.1038/nrg1325
    • (2004) Nat Rev Genet , vol.5 , pp. 335-344
    • Shendure, J.1    Mitra, R.D.2    Varma, C.3    Church, G.M.4
  • 59
    • 0021779934 scopus 로고
    • Measurements of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats
    • 10.1146/annurev.mi.39.100185.001541
    • JT Staley A Konopka 1985 Measurements of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats Annu Rev Microbiol 39 321 346 10.1146/annurev.mi.39.100185.001541
    • (1985) Annu Rev Microbiol , vol.39 , pp. 321-346
    • Staley, J.T.1    Konopka, A.2
  • 61
    • 33845874101 scopus 로고    scopus 로고
    • An obesity-associated gut microbiome with increased capacity for energy harvest
    • 10.1038/nature05414
    • PJ Turnbaugh RE Ley MA Mahowald V Magrini ER Mardis JI Gordon 2006 An obesity-associated gut microbiome with increased capacity for energy harvest Nature 444 1027 1031 10.1038/nature05414
    • (2006) Nature , vol.444 , pp. 1027-1031
    • Turnbaugh, P.J.1    Ley, R.E.2    Mahowald, M.A.3    Magrini, V.4    Mardis, E.R.5    Gordon, J.I.6
  • 66
    • 35148876440 scopus 로고    scopus 로고
    • Metagenomic analysis of the microbial community associated with the coral Porites astreoides
    • 10.1111/j.1462-2920.2007.01383.x
    • L Wegley R Edwards B Rodriguez-Brito H Liu F Rohwer 2007 Metagenomic analysis of the microbial community associated with the coral Porites astreoides Environ Microbiol 9 2707 2719 10.1111/j.1462-2920.2007.01383.x
    • (2007) Environ Microbiol , vol.9 , pp. 2707-2719
    • Wegley, L.1    Edwards, R.2    Rodriguez-Brito, B.3    Liu, H.4    Rohwer, F.5


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