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Volumn 8, Issue 12, 2012, Pages

Chapter 12: Human Microbiome Analysis

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL; BIOINFORMATIC TOOLS; BODY SURFACE; CONDITION; HIGH-THROUGHPUT SEQUENCING; HUMAN MICROBIOME; HUMAN MICROBIOTA; INFLAMMATORY BOWEL DISEASE; MICROBIOME; THERAPEUTIC INTERVENTION;

EID: 84872034370     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002808     Document Type: Article
Times cited : (367)

References (172)
  • 1
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1    Li, R.2    Raes, J.3    Arumugam, M.4    Burgdorf, K.S.5
  • 2
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.
    • Nature , vol.486 , pp. 207-214
  • 3
    • 0000631895 scopus 로고
    • Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten
    • Gram HC, (1884) Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten. Fortschritte der Medizin 2: 185-189.
    • (1884) Fortschritte Der Medizin , vol.2 , pp. 185-189
    • Gram, H.C.1
  • 5
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann RI, Ludwig W, Schleifer KH, (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
    • (1995) Microbiol Rev , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 6
    • 10344227692 scopus 로고    scopus 로고
    • Metagenomics: application of genomics to uncultured microorganisms
    • Handelsman J, (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669-685.
    • (2004) Microbiol Mol Biol Rev , vol.68 , pp. 669-685
    • Handelsman, J.1
  • 7
    • 0016800090 scopus 로고
    • A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase
    • Sanger F, Coulson AR, (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of molecular biology 94: 441-448.
    • (1975) Journal of Molecular Biology , vol.94 , pp. 441-448
    • Sanger, F.1    Coulson, A.R.2
  • 9
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3    Guigo, R.4    Gingeras, T.R.5
  • 10
    • 0029587036 scopus 로고
    • Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences
    • Bocchetta M, Ceccarelli E, Creti R, Sanangelantoni AM, Tiboni O, et al. (1995) Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences. J Mol Evol 41: 803-812.
    • (1995) J Mol Evol , vol.41 , pp. 803-812
    • Bocchetta, M.1    Ceccarelli, E.2    Creti, R.3    Sanangelantoni, A.M.4    Tiboni, O.5
  • 11
    • 0008048504 scopus 로고
    • Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
    • Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, et al. (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A 82: 6955-6959.
    • (1985) Proc Natl Acad Sci U S A , vol.82 , pp. 6955-6959
    • Lane, D.J.1    Pace, B.2    Olsen, G.J.3    Stahl, D.A.4    Sogin, M.L.5
  • 12
    • 84920629237 scopus 로고    scopus 로고
    • A renaissance for the pioneering 16S rRNA gene
    • Tringe SG, Hugenholtz P, (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11: 442-446.
    • (2008) Curr Opin Microbiol , vol.11 , pp. 442-446
    • Tringe, S.G.1    Hugenholtz, P.2
  • 14
    • 33746061683 scopus 로고    scopus 로고
    • Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    • DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 5069-5072
    • DeSantis, T.Z.1    Hugenholtz, P.2    Larsen, N.3    Rojas, M.4    Brodie, E.L.5
  • 15
    • 58149200948 scopus 로고    scopus 로고
    • The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
    • Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-145.
    • (2009) Nucleic Acids Res , vol.37
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3    Fish, J.4    Chai, B.5
  • 16
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
    • (2007) Nucleic Acids Res , vol.35 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3    Fuchs, B.M.4    Ludwig, W.5
  • 17
    • 43849089834 scopus 로고    scopus 로고
    • Microbial diversity and the genetic nature of microbial species
    • Achtman M, Wagner M, (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6: 431-440.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 431-440
    • Achtman, M.1    Wagner, M.2
  • 18
    • 78049240050 scopus 로고    scopus 로고
    • The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies
    • Schloss PD, (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.
    • (2010) PLoS Comput Biol , vol.6
    • Schloss, P.D.1
  • 19
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3    Hall, J.R.4    Hartmann, M.5
  • 20
    • 73449128271 scopus 로고    scopus 로고
    • Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    • Hamady M, Lozupone C, Knight R, (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27.
    • (2010) ISME J , vol.4 , pp. 17-27
    • Hamady, M.1    Lozupone, C.2    Knight, R.3
  • 21
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 22
    • 67650021209 scopus 로고    scopus 로고
    • Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
    • Hamady M, Knight R, (2009) Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res 19: 1141-1152.
    • (2009) Genome Res , vol.19 , pp. 1141-1152
    • Hamady, M.1    Knight, R.2
  • 24
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: a new phylogenetic method for comparing microbial communities
    • Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 28
    • 0001463548 scopus 로고
    • Nonparametric estimation of the number of classes in a population
    • Chao A, (1984) Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11: 265-270.
    • (1984) Scandinavian Journal of Statistics , vol.11 , pp. 265-270
    • Chao, A.1
  • 29
    • 77957888370 scopus 로고
    • Stopping rules and estimation for recapture debugging with unequal failure rates
    • Chao A, Ma M-C, Yang MCK, (1993) Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 80: 193-201.
    • (1993) Biometrika , vol.80 , pp. 193-201
    • Chao, A.1    Ma, M.-C.2    Yang, M.C.K.3
  • 30
    • 0020975097 scopus 로고
    • Estimating species richness using the jackknife procedure
    • Heltshe JF, Forrester NE, (1983) Estimating species richness using the jackknife procedure. Biometrics 39: 1-11.
    • (1983) Biometrics , vol.39 , pp. 1-11
    • Heltshe, J.F.1    Forrester, N.E.2
  • 31
    • 0028782130 scopus 로고
    • Estimating terrestrial biodiversity through extrapolation
    • Colwell RK, Coddington JA, (1994) Estimating terrestrial biodiversity through extrapolation. Phil Trans R Soc London B 345: 101-118.
    • (1994) Phil Trans R Soc London B , vol.345 , pp. 101-118
    • Colwell, R.K.1    Coddington, J.A.2
  • 32
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • Shannon CE, (1948) A mathematical theory of communication. Bell System Technical Journal 27: 379-656, 379-423, 623-656.
    • (1948) Bell System Technical Journal , vol.27 , pp. 379-656
    • Shannon, C.E.1
  • 33
    • 33344464667 scopus 로고
    • Measurement of diversity
    • Simpson EH, (1949) Measurement of diversity. Nature 163: 688.
    • (1949) Nature , vol.163 , pp. 688
    • Simpson, E.H.1
  • 34
    • 0000286531 scopus 로고
    • An ordination of upland forest communities of southern Wisconsin
    • Bray JR, Curtis JT, (1957) An ordination of upland forest communities of southern Wisconsin. Ecological Monographs 27: 325-349.
    • (1957) Ecological Monographs , vol.27 , pp. 325-349
    • Bray, J.R.1    Curtis, J.T.2
  • 35
    • 5044240973 scopus 로고    scopus 로고
    • Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
    • Huber T, Faulkner G, Hugenholtz P, (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.
    • (2004) Bioinformatics , vol.20 , pp. 2317-2319
    • Huber, T.1    Faulkner, G.2    Hugenholtz, P.3
  • 36
    • 33748805463 scopus 로고    scopus 로고
    • Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation
    • Brodie EL, Desantis TZ, Joyner DC, Baek SM, Larsen JT, et al. (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72: 6288-6298.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 6288-6298
    • Brodie, E.L.1    Desantis, T.Z.2    Joyner, D.C.3    Baek, S.M.4    Larsen, J.T.5
  • 37
    • 77955934408 scopus 로고    scopus 로고
    • Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray
    • Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, et al. (2010) Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Appl Environ Microbiol 76: 5636-5638.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 5636-5638
    • Schatz, M.C.1    Phillippy, A.M.2    Gajer, P.3    DeSantis, T.Z.4    Andersen, G.L.5
  • 38
    • 10944226351 scopus 로고    scopus 로고
    • Metagenomics: genomic analysis of microbial communities
    • Riesenfeld CS, Schloss PD, Handelsman J, (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38: 525-552.
    • (2004) Annu Rev Genet , vol.38 , pp. 525-552
    • Riesenfeld, C.S.1    Schloss, P.D.2    Handelsman, J.3
  • 39
    • 55449131166 scopus 로고    scopus 로고
    • Bioinformatics for whole-genome shotgun sequencing of microbial communities
    • Chen K, Pachter L, (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 1: 106-112.
    • (2005) PLoS Comput Biol , vol.1 , pp. 106-112
    • Chen, K.1    Pachter, L.2
  • 40
    • 52449114817 scopus 로고    scopus 로고
    • Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
    • Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3: e3042.
    • (2008) PLoS One , vol.3
    • Gilbert, J.A.1    Field, D.2    Huang, Y.3    Edwards, R.4    Li, W.5
  • 41
    • 77955963505 scopus 로고    scopus 로고
    • Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed
    • Booijink CC, Boekhorst J, Zoetendal EG, Smidt H, Kleerebezem M, et al. (2010) Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol 76: 5533-5540.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 5533-5540
    • Booijink, C.C.1    Boekhorst, J.2    Zoetendal, E.G.3    Smidt, H.4    Kleerebezem, M.5
  • 43
    • 81455144570 scopus 로고    scopus 로고
    • A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface
    • Li X, LeBlanc J, Truong A, Vuthoori R, Chen SS, et al. (2011) A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface. PLoS One 6: e26542.
    • (2011) PLoS One , vol.6
    • Li, X.1    LeBlanc, J.2    Truong, A.3    Vuthoori, R.4    Chen, S.S.5
  • 44
    • 52649090774 scopus 로고    scopus 로고
    • An invitation to the marriage of metagenomics and metabolomics
    • Turnbaugh PJ, Gordon JI, (2008) An invitation to the marriage of metagenomics and metabolomics. Cell 134: 708-713.
    • (2008) Cell , vol.134 , pp. 708-713
    • Turnbaugh, P.J.1    Gordon, J.I.2
  • 45
    • 62649151803 scopus 로고    scopus 로고
    • Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
    • Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, et al. (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci U S A 106: 3698-3703.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 3698-3703
    • Wikoff, W.R.1    Anfora, A.T.2    Liu, J.3    Schultz, P.G.4    Lesley, S.A.5
  • 46
    • 31944437874 scopus 로고    scopus 로고
    • Metaproteomics: studying functional gene expression in microbial ecosystems
    • Wilmes P, Bond PL, (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14: 92-97.
    • (2006) Trends Microbiol , vol.14 , pp. 92-97
    • Wilmes, P.1    Bond, P.L.2
  • 47
    • 66649089244 scopus 로고    scopus 로고
    • Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre
    • Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, et al. (2009) Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11: 1358-1375.
    • (2009) Environ Microbiol , vol.11 , pp. 1358-1375
    • Poretsky, R.S.1    Hewson, I.2    Sun, S.3    Allen, A.E.4    Zehr, J.P.5
  • 48
    • 66149130975 scopus 로고    scopus 로고
    • Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
    • Shi Y, Tyson GW, DeLong EF, (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459: 266-269.
    • (2009) Nature , vol.459 , pp. 266-269
    • Shi, Y.1    Tyson, G.W.2    DeLong, E.F.3
  • 49
    • 84858990515 scopus 로고    scopus 로고
    • Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
    • Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, et al. (2012) Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome biology 13: R23.
    • (2012) Genome Biology , vol.13
    • Giannoukos, G.1    Ciulla, D.M.2    Huang, K.3    Haas, B.J.4    Izard, J.5
  • 52
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • A framework for human microbiome research. Nature 486: 215-221.
    • Nature , vol.486 , pp. 215-221
  • 53
    • 1542377296 scopus 로고    scopus 로고
    • Community structure and metabolism through reconstruction of microbial genomes from the environment
    • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
    • (2004) Nature , vol.428 , pp. 37-43
    • Tyson, G.W.1    Chapman, J.2    Hugenholtz, P.3    Allen, E.E.4    Ram, R.J.5
  • 55
    • 52949115612 scopus 로고    scopus 로고
    • Microbiology: metagenomics
    • Hugenholtz P, Tyson GW, (2008) Microbiology: metagenomics. Nature 455: 481-483.
    • (2008) Nature , vol.455 , pp. 481-483
    • Hugenholtz, P.1    Tyson, G.W.2
  • 58
    • 34249794257 scopus 로고    scopus 로고
    • Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
    • Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, et al. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 4: 495-500.
    • (2007) Nat Methods , vol.4 , pp. 495-500
    • Mavromatis, K.1    Ivanova, N.2    Barry, K.3    Shapiro, H.4    Goltsman, E.5
  • 60
  • 62
    • 78651326786 scopus 로고    scopus 로고
    • FragGeneScan: predicting genes in short and error-prone reads
    • Rho M, Tang H, Ye Y, (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res.
    • (2010) Nucleic Acids Res
    • Rho, M.1    Tang, H.2    Ye, Y.3
  • 64
    • 77950814686 scopus 로고    scopus 로고
    • Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
    • Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, et al. (2010) Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC Genomics 11: 242.
    • (2010) BMC Genomics , vol.11 , pp. 242
    • Nagarajan, N.1    Cook, C.2    Di Bonaventura, M.3    Ge, H.4    Richards, A.5
  • 65
    • 67449095888 scopus 로고    scopus 로고
    • Genome assembly reborn: recent computational challenges
    • Pop M, (2009) Genome assembly reborn: recent computational challenges. Brief Bioinform 10: 354-366.
    • (2009) Brief Bioinform , vol.10 , pp. 354-366
    • Pop, M.1
  • 67
    • 4344670204 scopus 로고    scopus 로고
    • Application of tetranucleotide frequencies for the assignment of genomic fragments
    • Teeling H, Meyerdierks A, Bauer M, Amann R, Glockner FO, (2004) Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 6: 938-947.
    • (2004) Environ Microbiol , vol.6 , pp. 938-947
    • Teeling, H.1    Meyerdierks, A.2    Bauer, M.3    Amann, R.4    Glockner, F.O.5
  • 69
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • Brady A, Salzberg SL, (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 6: 673-676.
    • (2009) Nat Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 71
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 74
    • 78149262230 scopus 로고    scopus 로고
    • Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes
    • Veiga P, Gallini CA, Beal C, Michaud M, Delaney ML, et al. (2010) Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes. Proc Natl Acad Sci U S A.
    • (2010) Proc Natl Acad Sci U S A
    • Veiga, P.1    Gallini, C.A.2    Beal, C.3    Michaud, M.4    Delaney, M.L.5
  • 76
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.M.5
  • 77
    • 77957761759 scopus 로고    scopus 로고
    • METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics
    • Goll J, Rusch D, Tanenbaum DM, Thiagarajan M, Li K, et al. (2010) METAREP: JCVI Metagenomics Reports- an open source tool for high-performance comparative metagenomics. Bioinformatics.
    • (2010) Bioinformatics
    • Goll, J.1    Rusch, D.2    Tanenbaum, D.M.3    Thiagarajan, M.4    Li, K.5
  • 78
    • 33947221422 scopus 로고    scopus 로고
    • Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes
    • Eisen JA, (2007) Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol 5: e82.
    • (2007) PLoS Biol , vol.5
    • Eisen, J.A.1
  • 79
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 80
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R, (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 82
    • 33947238287 scopus 로고    scopus 로고
    • The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
    • Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
    • (2007) PLoS Biol , vol.5
    • Rusch, D.B.1    Halpern, A.L.2    Sutton, G.3    Heidelberg, K.B.4    Williamson, S.5
  • 83
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 84
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-360.
    • (2010) Nucleic Acids Res , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 85
    • 0033194958 scopus 로고    scopus 로고
    • Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB), Enzyme Supplement 5 (1999)
    • NC-IUBMB
    • NC-IUBMB (1999) Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB), Enzyme Supplement 5 (1999). Eur J Biochem 264: 610-650.
    • (1999) Eur J Biochem , vol.264 , pp. 610-650
  • 86
    • 33846040629 scopus 로고    scopus 로고
    • TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
    • Ren Q, Chen K, Paulsen IT, (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 35: D274-279.
    • (2007) Nucleic Acids Res , vol.35
    • Ren, Q.1    Chen, K.2    Paulsen, I.T.3
  • 87
    • 34248531753 scopus 로고    scopus 로고
    • Locating proteins in the cell using TargetP, SignalP and related tools
    • Emanuelsson O, Brunak S, von Heijne G, Nielsen H, (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2: 953-971.
    • (2007) Nat Protoc , vol.2 , pp. 953-971
    • Emanuelsson, O.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 90
    • 75549085495 scopus 로고    scopus 로고
    • eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
    • Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, et al. (2010) eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 38: D190-195.
    • (2010) Nucleic Acids Res , vol.38
    • Muller, J.1    Szklarczyk, D.2    Julien, P.3    Letunic, I.4    Roth, A.5
  • 91
    • 75549090505 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 38: D473-479.
    • (2010) Nucleic Acids Res , vol.38
    • Caspi, R.1    Altman, T.2    Dale, J.M.3    Dreher, K.4    Fulcher, C.A.5
  • 93
    • 3242719687 scopus 로고    scopus 로고
    • Phosphoenolpyruvate carboxylase: a new era of structural biology
    • Izui K, Matsumura H, Furumoto T, Kai Y, (2004) Phosphoenolpyruvate carboxylase: a new era of structural biology. Annu Rev Plant Biol 55: 69-84.
    • (2004) Annu Rev Plant Biol , vol.55 , pp. 69-84
    • Izui, K.1    Matsumura, H.2    Furumoto, T.3    Kai, Y.4
  • 95
    • 70049085269 scopus 로고    scopus 로고
    • A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes
    • Ye Y, Doak TG, (2009) A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol 5: e1000465.
    • (2009) PLoS Comput Biol , vol.5
    • Ye, Y.1    Doak, T.G.2
  • 97
    • 34547676311 scopus 로고    scopus 로고
    • Optimization based automated curation of metabolic reconstructions
    • Satish Kumar V, Dasika MS, Maranas CD, (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8: 212.
    • (2007) BMC Bioinformatics , vol.8 , pp. 212
    • Satish Kumar, V.1    Dasika, M.S.2    Maranas, C.D.3
  • 98
    • 13244268322 scopus 로고    scopus 로고
    • A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    • Green ML, Karp PD, (2004) A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5: 76.
    • (2004) BMC Bioinformatics , vol.5 , pp. 76
    • Green, M.L.1    Karp, P.D.2
  • 99
    • 57549102595 scopus 로고    scopus 로고
    • Genome-scale models of bacterial metabolism: reconstruction and applications
    • Durot M, Bourguignon PY, Schachter V, (2009) Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 33: 164-190.
    • (2009) FEMS Microbiol Rev , vol.33 , pp. 164-190
    • Durot, M.1    Bourguignon, P.Y.2    Schachter, V.3
  • 100
    • 57049122827 scopus 로고    scopus 로고
    • "Omics" data and levels of evidence for biomarker discovery
    • Ghosh D, Poisson LM, (2009) "Omics" data and levels of evidence for biomarker discovery. Genomics 93: 13-16.
    • (2009) Genomics , vol.93 , pp. 13-16
    • Ghosh, D.1    Poisson, L.M.2
  • 101
    • 13144306071 scopus 로고    scopus 로고
    • Genome-wide association studies for common diseases and complex traits
    • Hirschhorn JN, Daly MJ, (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6: 95-108.
    • (2005) Nat Rev Genet , vol.6 , pp. 95-108
    • Hirschhorn, J.N.1    Daly, M.J.2
  • 103
    • 77949495880 scopus 로고    scopus 로고
    • Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
    • Tepper N, Shlomi T, (2010) Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 26: 536-543.
    • (2010) Bioinformatics , vol.26 , pp. 536-543
    • Tepper, N.1    Shlomi, T.2
  • 105
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I, Palsson BO, (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5: 93-121.
    • (2010) Nat Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 106
    • 19144366814 scopus 로고    scopus 로고
    • Metagenomics and industrial applications
    • Lorenz P, Eck J, (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3: 510-516.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 510-516
    • Lorenz, P.1    Eck, J.2
  • 107
    • 77951134703 scopus 로고    scopus 로고
    • A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion
    • Sommer MO, Church GM, Dantas G, (2010) A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Mol Syst Biol 6: 360.
    • (2010) Mol Syst Biol , vol.6 , pp. 360
    • Sommer, M.O.1    Church, G.M.2    Dantas, G.3
  • 111
    • 77957979642 scopus 로고    scopus 로고
    • Comparative metagenomics and population dynamics of the gut microbiota in mother and infant
    • Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, et al. (2010) Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol 2010: 53-66.
    • (2010) Genome Biol Evol , vol.2010 , pp. 53-66
    • Vaishampayan, P.A.1    Kuehl, J.V.2    Froula, J.L.3    Morgan, J.L.4    Ochman, H.5
  • 112
    • 76349092715 scopus 로고    scopus 로고
    • Convergent temporal dynamics of the human infant gut microbiota
    • Trosvik P, Stenseth NC, Rudi K, (2010) Convergent temporal dynamics of the human infant gut microbiota. ISME J 4: 151-158.
    • (2010) ISME J , vol.4 , pp. 151-158
    • Trosvik, P.1    Stenseth, N.C.2    Rudi, K.3
  • 113
    • 38849190556 scopus 로고    scopus 로고
    • Gut microbiota: a potential new territory for drug targeting
    • Jia W, Li H, Zhao L, Nicholson JK, (2008) Gut microbiota: a potential new territory for drug targeting. Nat Rev Drug Discov 7: 123-129.
    • (2008) Nat Rev Drug Discov , vol.7 , pp. 123-129
    • Jia, W.1    Li, H.2    Zhao, L.3    Nicholson, J.K.4
  • 114
    • 67349250428 scopus 로고    scopus 로고
    • The gut microbiota shapes intestinal immune responses during health and disease
    • Round JL, Mazmanian SK, (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9: 313-323.
    • (2009) Nat Rev Immunol , vol.9 , pp. 313-323
    • Round, J.L.1    Mazmanian, S.K.2
  • 115
    • 66349083859 scopus 로고    scopus 로고
    • Topographical and temporal diversity of the human skin microbiome
    • Grice EA, Kong HH, Conlan S, Deming CB, Davis J, et al. (2009) Topographical and temporal diversity of the human skin microbiome. Science 324: 1190-1192.
    • (2009) Science , vol.324 , pp. 1190-1192
    • Grice, E.A.1    Kong, H.H.2    Conlan, S.3    Deming, C.B.4    Davis, J.5
  • 117
    • 84862162269 scopus 로고    scopus 로고
    • Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
    • Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, et al. (2012) Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome biology 13: R42.
    • (2012) Genome Biology , vol.13
    • Segata, N.1    Haake, S.K.2    Mannon, P.3    Lemon, K.P.4    Waldron, L.5
  • 119
    • 0037425743 scopus 로고    scopus 로고
    • Gut flora in health and disease
    • Guarner F, Malagelada JR, (2003) Gut flora in health and disease. Lancet 361: 512-519.
    • (2003) Lancet , vol.361 , pp. 512-519
    • Guarner, F.1    Malagelada, J.R.2
  • 120
    • 70449703996 scopus 로고    scopus 로고
    • What are the consequences of the disappearing human microbiota?
    • Blaser MJ, Falkow S, (2009) What are the consequences of the disappearing human microbiota? Nat Rev Microbiol 7: 887-894.
    • (2009) Nat Rev Microbiol , vol.7 , pp. 887-894
    • Blaser, M.J.1    Falkow, S.2
  • 121
    • 77955386857 scopus 로고    scopus 로고
    • Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
    • Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, et al. (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 107: 11971-11975.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 11971-11975
    • Dominguez-Bello, M.G.1    Costello, E.K.2    Contreras, M.3    Magris, M.4    Hidalgo, G.5
  • 122
  • 123
    • 77955292433 scopus 로고    scopus 로고
    • Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients
    • Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, et al. (2010) Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One 5: e11044.
    • (2010) PLoS One , vol.5
    • Cox, M.J.1    Allgaier, M.2    Taylor, B.3    Baek, M.S.4    Huang, Y.J.5
  • 124
    • 17844404232 scopus 로고    scopus 로고
    • Gut microorganisms, mammalian metabolism and personalized health care
    • Nicholson JK, Holmes E, Wilson ID, (2005) Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 3: 431-438.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 431-438
    • Nicholson, J.K.1    Holmes, E.2    Wilson, I.D.3
  • 125
    • 77950353786 scopus 로고    scopus 로고
    • Homeostasis and inflammation in the intestine
    • Garrett WS, Gordon JI, Glimcher LH, (2010) Homeostasis and inflammation in the intestine. Cell 140: 859-870.
    • (2010) Cell , vol.140 , pp. 859-870
    • Garrett, W.S.1    Gordon, J.I.2    Glimcher, L.H.3
  • 126
    • 78649697578 scopus 로고    scopus 로고
    • Microbes and Health Sackler Colloquium: Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
    • Dethlefsen L, Relman DA, (2010) Microbes and Health Sackler Colloquium: Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A.
    • (2010) Proc Natl Acad Sci U S A
    • Dethlefsen, L.1    Relman, D.A.2
  • 127
    • 56849106496 scopus 로고    scopus 로고
    • The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    • Dethlefsen L, Huse S, Sogin ML, Relman DA, (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6: e280.
    • (2008) PLoS Biol , vol.6
    • Dethlefsen, L.1    Huse, S.2    Sogin, M.L.3    Relman, D.A.4
  • 129
    • 38449088143 scopus 로고    scopus 로고
    • Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
    • Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14: 169-181.
    • (2007) DNA Res , vol.14 , pp. 169-181
    • Kurokawa, K.1    Itoh, T.2    Kuwahara, T.3    Oshima, K.4    Toh, H.5
  • 130
    • 79952270399 scopus 로고    scopus 로고
    • Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome
    • Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, et al. (2010) Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A.
    • (2010) Proc Natl Acad Sci U S A
    • Koenig, J.E.1    Spor, A.2    Scalfone, N.3    Fricker, A.D.4    Stombaugh, J.5
  • 131
    • 79951680506 scopus 로고    scopus 로고
    • Microbes and Health Sackler Colloquium: Composition, variability, and temporal stability of the intestinal microbiota of the elderly
    • Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, et al. (2010) Microbes and Health Sackler Colloquium: Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A.
    • (2010) Proc Natl Acad Sci U S A
    • Claesson, M.J.1    Cusack, S.2    O'Sullivan, O.3    Greene-Diniz, R.4    de Weerd, H.5
  • 132
    • 84864722033 scopus 로고    scopus 로고
    • Gut microbiota composition correlates with diet and health in the elderly
    • Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, et al. (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488: 178-184.
    • (2012) Nature , vol.488 , pp. 178-184
    • Claesson, M.J.1    Jeffery, I.B.2    Conde, S.3    Power, S.E.4    O'Connor, E.M.5
  • 133
    • 80053618114 scopus 로고    scopus 로고
    • Linking long-term dietary patterns with gut microbial enterotypes
    • Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, et al. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334: 105-108.
    • (2011) Science , vol.334 , pp. 105-108
    • Wu, G.D.1    Chen, J.2    Hoffmann, C.3    Bittinger, K.4    Chen, Y.Y.5
  • 134
    • 79952316380 scopus 로고    scopus 로고
    • Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency
    • Spencer MD, Hamp TJ, Reid RW, Fischer LM, Zeisel SH, et al. (2011) Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 140: 976-986.
    • (2011) Gastroenterology , vol.140 , pp. 976-986
    • Spencer, M.D.1    Hamp, T.J.2    Reid, R.W.3    Fischer, L.M.4    Zeisel, S.H.5
  • 135
    • 76349111356 scopus 로고    scopus 로고
    • Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice
    • Zhang C, Zhang M, Wang S, Han R, Cao Y, et al. (2010) Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J 4: 232-241.
    • (2010) ISME J , vol.4 , pp. 232-241
    • Zhang, C.1    Zhang, M.2    Wang, S.3    Han, R.4    Cao, Y.5
  • 136
    • 35348961403 scopus 로고    scopus 로고
    • An ecological and evolutionary perspective on human-microbe mutualism and disease
    • Dethlefsen L, McFall-Ngai M, Relman DA, (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449: 811-818.
    • (2007) Nature , vol.449 , pp. 811-818
    • Dethlefsen, L.1    McFall-Ngai, M.2    Relman, D.A.3
  • 137
    • 79956301905 scopus 로고    scopus 로고
    • Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans
    • Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, et al. (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332: 970-974.
    • (2011) Science , vol.332 , pp. 970-974
    • Muegge, B.D.1    Kuczynski, J.2    Knights, D.3    Clemente, J.C.4    Gonzalez, A.5
  • 138
    • 33845901507 scopus 로고    scopus 로고
    • Microbial ecology: human gut microbes associated with obesity
    • Ley RE, Turnbaugh PJ, Klein S, Gordon JI, (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
    • (2006) Nature , vol.444 , pp. 1022-1023
    • Ley, R.E.1    Turnbaugh, P.J.2    Klein, S.3    Gordon, J.I.4
  • 140
    • 33745610880 scopus 로고    scopus 로고
    • A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism
    • Samuel BS, Gordon JI, (2006) A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A 103: 10011-10016.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 10011-10016
    • Samuel, B.S.1    Gordon, J.I.2
  • 141
    • 1842532897 scopus 로고    scopus 로고
    • Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota
    • Rawls JF, Samuel BS, Gordon JI, (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci U S A 101: 4596-4601.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 4596-4601
    • Rawls, J.F.1    Samuel, B.S.2    Gordon, J.I.3
  • 142
    • 33749997498 scopus 로고    scopus 로고
    • Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection
    • Rawls JF, Mahowald MA, Ley RE, Gordon JI, (2006) Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127: 423-433.
    • (2006) Cell , vol.127 , pp. 423-433
    • Rawls, J.F.1    Mahowald, M.A.2    Ley, R.E.3    Gordon, J.I.4
  • 143
    • 70350343544 scopus 로고    scopus 로고
    • Induction of intestinal Th17 cells by segmented filamentous bacteria
    • Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, et al. (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139: 485-498.
    • (2009) Cell , vol.139 , pp. 485-498
    • Ivanov, I.I.1    Atarashi, K.2    Manel, N.3    Brodie, E.L.4    Shima, T.5
  • 144
    • 77951480203 scopus 로고    scopus 로고
    • Segmented filamentous bacteria take the stage
    • Ivanov, II, Littman DR, (2010) Segmented filamentous bacteria take the stage. Mucosal Immunol 3: 209-212.
    • (2010) Mucosal Immunol , vol.3 , pp. 209-212
    • Ivanov, I.I.1    Littman, D.R.2
  • 145
    • 77950669604 scopus 로고    scopus 로고
    • The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice
    • Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, et al. (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1: 6ra14.
    • (2009) Sci Transl Med , vol.1
    • Turnbaugh, P.J.1    Ridaura, V.K.2    Faith, J.J.3    Rey, F.E.4    Knight, R.5
  • 146
    • 74249119678 scopus 로고    scopus 로고
    • Obesity and the human microbiome
    • Ley RE, (2010) Obesity and the human microbiome. Curr Opin Gastroenterol 26: 5-11.
    • (2010) Curr Opin Gastroenterol , vol.26 , pp. 5-11
    • Ley, R.E.1
  • 147
    • 33845874101 scopus 로고    scopus 로고
    • An obesity-associated gut microbiome with increased capacity for energy harvest
    • Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
    • (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
  • 148
    • 41849127118 scopus 로고    scopus 로고
    • Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
    • Turnbaugh PJ, Backhed F, Fulton L, Gordon JI, (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3: 213-223.
    • (2008) Cell Host Microbe , vol.3 , pp. 213-223
    • Turnbaugh, P.J.1    Backhed, F.2    Fulton, L.3    Gordon, J.I.4
  • 149
    • 34247237888 scopus 로고    scopus 로고
    • Dental plaque as a biofilm and a microbial community - implications for health and disease
    • Marsh PD, (2006) Dental plaque as a biofilm and a microbial community- implications for health and disease. BMC Oral Health 6(Suppl 1):: S14.
    • (2006) BMC Oral Health , vol.6 , Issue.SUPPL. 1
    • Marsh, P.D.1
  • 152
    • 0035289823 scopus 로고    scopus 로고
    • Spatial arrangements and associative behavior of species in an in vitro oral biofilm model
    • Guggenheim M, Shapiro S, Gmur R, Guggenheim B, (2001) Spatial arrangements and associative behavior of species in an in vitro oral biofilm model. Appl Environ Microbiol 67: 1343-1350.
    • (2001) Appl Environ Microbiol , vol.67 , pp. 1343-1350
    • Guggenheim, M.1    Shapiro, S.2    Gmur, R.3    Guggenheim, B.4
  • 153
    • 37549045059 scopus 로고    scopus 로고
    • Streptococcal receptor polysaccharides: recognition molecules for oral biofilm formation
    • Yoshida Y, Palmer RJ, Yang J, Kolenbrander PE, Cisar JO, (2006) Streptococcal receptor polysaccharides: recognition molecules for oral biofilm formation. BMC Oral Health 6(Suppl 1):: S12.
    • (2006) BMC Oral Health , vol.6 , Issue.SUPPL. 1
    • Yoshida, Y.1    Palmer, R.J.2    Yang, J.3    Kolenbrander, P.E.4    Cisar, J.O.5
  • 154
    • 27844560086 scopus 로고    scopus 로고
    • Oral microbial communities in sickness and in health
    • Jenkinson HF, Lamont RJ, (2005) Oral microbial communities in sickness and in health. Trends Microbiol 13: 589-595.
    • (2005) Trends Microbiol , vol.13 , pp. 589-595
    • Jenkinson, H.F.1    Lamont, R.J.2
  • 156
    • 77950847866 scopus 로고    scopus 로고
    • Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
    • Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, et al. (2010) Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464: 908-912.
    • (2010) Nature , vol.464 , pp. 908-912
    • Hehemann, J.H.1    Correc, G.2    Barbeyron, T.3    Helbert, W.4    Czjzek, M.5
  • 157
    • 69949108799 scopus 로고    scopus 로고
    • The role of the intestinal microbiota in enteric infection
    • Sekirov I, Finlay BB, (2009) The role of the intestinal microbiota in enteric infection. J Physiol 587: 4159-4167.
    • (2009) J Physiol , vol.587 , pp. 4159-4167
    • Sekirov, I.1    Finlay, B.B.2
  • 158
    • 33745128028 scopus 로고    scopus 로고
    • The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution
    • van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K, et al. (2006) The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci U S A 103: 9274-9279.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 9274-9279
    • van de Guchte, M.1    Penaud, S.2    Grimaldi, C.3    Barbe, V.4    Bryson, K.5
  • 159
    • 38349078772 scopus 로고    scopus 로고
    • Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model
    • Martin FP, Wang Y, Sprenger N, Yap IK, Lundstedt T, et al. (2008) Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. Mol Syst Biol 4: 157.
    • (2008) Mol Syst Biol , vol.4 , pp. 157
    • Martin, F.P.1    Wang, Y.2    Sprenger, N.3    Yap, I.K.4    Lundstedt, T.5
  • 160
    • 33745594044 scopus 로고    scopus 로고
    • The gut flora as a forgotten organ
    • O'Hara AM, Shanahan F, (2006) The gut flora as a forgotten organ. EMBO Rep 7: 688-693.
    • (2006) EMBO Rep , vol.7 , pp. 688-693
    • O'Hara, A.M.1    Shanahan, F.2
  • 161
    • 79955876063 scopus 로고    scopus 로고
    • How Microbes Defend and Define Us
    • New York, NY
    • Zimmer C (2010) How Microbes Defend and Define Us. The New York Times. New York, NY.
    • (2010) The New York Times
    • Zimmer, C.1
  • 162
    • 77951700268 scopus 로고    scopus 로고
    • Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea
    • Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ, (2010) Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol 44: 354-360.
    • (2010) J Clin Gastroenterol , vol.44 , pp. 354-360
    • Khoruts, A.1    Dicksved, J.2    Jansson, J.K.3    Sadowsky, M.J.4
  • 163
    • 0033766138 scopus 로고    scopus 로고
    • "Flora Power"- fecal bacteria cure chronic C. difficile diarrhea
    • Borody TJ, (2000) "Flora Power"- fecal bacteria cure chronic C. difficile diarrhea. Am J Gastroenterol 95: 3028-3029.
    • (2000) Am J Gastroenterol , vol.95 , pp. 3028-3029
    • Borody, T.J.1
  • 164
    • 84863415937 scopus 로고    scopus 로고
    • Illumina-based analysis of microbial community diversity
    • Degnan PH, Ochman H, (2011) Illumina-based analysis of microbial community diversity. The ISME journal.
    • (2011) The ISME Journal
    • Degnan, P.H.1    Ochman, H.2
  • 166
    • 67650763443 scopus 로고    scopus 로고
    • Visual and statistical comparison of metagenomes
    • Mitra S, Klar B, Huson DH, (2009) Visual and statistical comparison of metagenomes. Bioinformatics 25: 1849-1855.
    • (2009) Bioinformatics , vol.25 , pp. 1849-1855
    • Mitra, S.1    Klar, B.2    Huson, D.H.3
  • 167
    • 0003924276 scopus 로고    scopus 로고
    • Microbial Ecology: Fundamentals and Applications: Benjamin Cummings
    • Atlas RM, Bartha R, (1997) Microbial Ecology: Fundamentals and Applications: Benjamin Cummings.
    • (1997)
    • Atlas, R.M.1    Bartha, R.2
  • 168
    • 0030982247 scopus 로고    scopus 로고
    • A molecular view of microbial diversity and the biosphere
    • Pace NR, (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
    • (1997) Science , vol.276 , pp. 734-740
    • Pace, N.R.1
  • 169
    • 49649089054 scopus 로고    scopus 로고
    • Molecular eco-systems biology: towards an understanding of community function
    • Raes J, Bork P, (2008) Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol 6: 693-699.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 693-699
    • Raes, J.1    Bork, P.2
  • 171
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1    Begley, T.2    Butler, R.M.3    Choudhuri, J.V.4    Chuang, H.Y.5
  • 172
    • 84871709986 scopus 로고    scopus 로고
    • Biodiversity and functional genomics in the human microbiome
    • doi:10.1016/j.tig.2012.09.005. Epub ahead of print 7 November 2012
    • Morgan XC, Segata N, Huttenhower C (in press) Biodiversity and functional genomics in the human microbiome. Trends Genet. doi:10.1016/j.tig.2012.09.005. Epub ahead of print 7 November 2012.
    • Trends Genet
    • Morgan, X.C.1    Segata, N.2    Huttenhower, C.3


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