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Volumn 9, Issue 1, 2015, Pages 68-80

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); OTUS;

EID: 84923545661     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2014.117     Document Type: Article
Times cited : (144)

References (43)
  • 1
    • 84879369738 scopus 로고    scopus 로고
    • Commensal bacteria at the interface of host metabolism and the immune system
    • Brestoff JR, Artis D. (2013). Commensal bacteria at the interface of host metabolism and the immune system. Nat Immunol 14: 676-684.
    • (2013) Nat Immunol , vol.14 , pp. 676-684
    • Brestoff, J.R.1    Artis, D.2
  • 3
    • 84863981120 scopus 로고    scopus 로고
    • Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N et al. (2012). Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6: 1621-1624.
    • (2012) ISME J , vol.6 , pp. 1621-1624
    • Caporaso, J.G.1    Lauber, C.L.2    Walters, W.A.3    Berg-Lyons, D.4    Huntley, J.5    Fierer, N.6
  • 4
  • 5
    • 84861992014 scopus 로고    scopus 로고
    • The application of ecological theory toward an understanding of the human microbiome
    • Costello EK, Stagaman K, Dethlefsen L, Bohannan BJM, Relman DA. (2012). The application of ecological theory toward an understanding of the human microbiome. Science 336: 1255-1262.
    • (2012) Science , vol.336 , pp. 1255-1262
    • Costello, E.K.1    Stagaman, K.2    Dethlefsen, L.3    Bjm, B.4    Relman, D.A.5
  • 6
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 8
    • 84884904719 scopus 로고    scopus 로고
    • UPARSE: Highly accurate OTU sequences from microbial amplicon reads
    • Edgar RC. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10: 996-998.
    • (2013) Nat Methods , vol.10 , pp. 996-998
    • Edgar, R.C.1
  • 9
    • 84889649570 scopus 로고    scopus 로고
    • Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data
    • Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG et al. (2013). Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol 4: 1111-1119.
    • (2013) Methods Ecol Evol , vol.4 , pp. 1111-1119
    • Eren, A.M.1    Maignien, L.2    Sul, W.J.3    Murphy, L.G.4    Grim, S.L.5    Morrison, H.G.6
  • 11
    • 79952751932 scopus 로고    scopus 로고
    • The generation and maintenance of diversity in microbial communities
    • Fierer N, Lennon JT. (2011). The generation and maintenance of diversity in microbial communities. Am J Bot 98: 439-448.
    • (2011) Am J Bot , vol.98 , pp. 439-448
    • Fierer, N.1    Lennon, J.T.2
  • 13
    • 79952006773 scopus 로고    scopus 로고
    • Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    • Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G et al. (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 3: 494-504.
    • (2011) Genome Res , vol.3 , pp. 494-504
    • Haas, B.J.1    Gevers, D.2    Earl, A.M.3    Feldgarden, M.4    Ward, D.V.5    Giannoukos, G.6
  • 14
    • 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
  • 15
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: A web server for clustering and comparing biological sequences
    • Huang Y, Niu BF, Gao Y, Fu LM, Li WZ. (2010). CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26: 680-682.
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1    Niu, B.F.2    Gao, Y.3    Fu, L.M.4    Li, W.Z.5
  • 16
    • 44449178480 scopus 로고    scopus 로고
    • Resource partitioning and sympatric differentiation among closely related bacterioplankton
    • Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF. (2008). Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320: 1081-1085.
    • (2008) Science , vol.320 , pp. 1081-1085
    • Hunt, D.E.1    David, L.A.2    Gevers, D.3    Preheim, S.P.4    Alm, E.J.5    Polz, M.F.6
  • 17
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse SM, Welch DM, Morrison HG, Sogin ML. (2010). Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12: 1889-1898.
    • (2010) Environ Microbiol , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 19
    • 84879343905 scopus 로고    scopus 로고
    • Control of pathogens and pathobionts by the gut microbiota
    • Kamada N, Chen GY, Inohara N, Nunez G. (2013). Control of pathogens and pathobionts by the gut microbiota. Nat Immunol 14: 685-690.
    • (2013) Nat Immunol , vol.14 , pp. 685-690
    • Kamada, N.1    Chen, G.Y.2    Inohara, N.3    Nunez, G.4
  • 20
    • 84871808499 scopus 로고    scopus 로고
    • Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
    • Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M et al. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41: e1.
    • (2013) Nucleic Acids Res , vol.41 , pp. e1
    • Klindworth, A.1    Pruesse, E.2    Schweer, T.3    Peplies, J.4    Quast, C.5    Horn, M.6
  • 21
    • 73349110099 scopus 로고    scopus 로고
    • Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
    • Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. (2010). Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
    • (2010) Environ Microbiol , vol.12 , pp. 118-123
    • Kunin, V.1    Engelbrektson, A.2    Ochman, H.3    Hugenholtz, P.4
  • 22
    • 84884127512 scopus 로고    scopus 로고
    • Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
    • Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnol 31: 814-821.
    • (2013) Nature Biotechnol , vol.31 , pp. 814-821
    • Mgi, L.1    Zaneveld, J.2    Caporaso, J.G.3    McDonald, D.4    Knights, D.5    Reyes, J.A.6
  • 23
    • 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
  • 24
  • 26
    • 0346726023 scopus 로고    scopus 로고
    • Neutral mutations and neutral substitutions in bacterial genomes
    • Ochman H. (2003). Neutral mutations and neutral substitutions in bacterial genomes. Mol Biol Evol 20: 2091-2096.
    • (2003) Mol Biol Evol , vol.20 , pp. 2091-2096
    • Ochman, H.1
  • 32
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: Opensource, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009). Introducing mothur: opensource, 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    Hollister, E.B.6
  • 33
    • 83355173006 scopus 로고    scopus 로고
    • Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    • Schloss PD, Gevers D, Westcott SL. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6: e27310.
    • (2011) PLoS One , vol.6 , pp. e27310
    • Schloss, P.D.1    Gevers, D.2    Westcott, S.L.3
  • 34
    • 79958196766 scopus 로고    scopus 로고
    • Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis
    • Schloss PD, Westcott SL. (2011). Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77: 3219-3226.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 3219-3226
    • Schloss, P.D.1    Westcott, S.L.2
  • 36
    • 84880917983 scopus 로고    scopus 로고
    • A meta-analysis of changes in bacterial and archaeal communities with time
    • Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N. (2013). A meta-analysis of changes in bacterial and archaeal communities with time. ISME J 7: 1493-1506.
    • (2013) ISME J , vol.7 , pp. 1493-1506
    • Shade, A.1    Caporaso, J.G.2    Handelsman, J.3    Knight, R.4    Fierer, N.5
  • 38
    • 80052300610 scopus 로고    scopus 로고
    • Bacterial community comparisons by taxonomy- supervised analysis independent of sequence alignment and clustering
    • Sul WJ, Cole JR, Jesus ED, Wang Q, Farris RJ, Fish JA et al. (2011). Bacterial community comparisons by taxonomy- supervised analysis independent of sequence alignment and clustering. Proc Natl Acad Sci USA 108: 14637-14642.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 14637-14642
    • Sul, W.J.1    Cole, J.R.2    Jesus, E.D.3    Wang, Q.4    Farris, R.J.5    Fish, J.A.6
  • 39
    • 3542994534 scopus 로고    scopus 로고
    • Copy number of ribosomal operons in prokaryotes and its effect on phylogenetic analyses
    • Tourova TP. (2003). Copy number of ribosomal operons in prokaryotes and its effect on phylogenetic analyses. Microbiology 72: 389-402.
    • (2003) Microbiology , vol.72 , pp. 389-402
    • Tourova, T.P.1
  • 40
    • 77952158672 scopus 로고    scopus 로고
    • Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
    • Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F et al. (2010). Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci USA 107: 7503-7508.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 7503-7508
    • Turnbaugh, P.J.1    Quince, C.2    Faith, J.J.3    McHardy, A.C.4    Yatsunenko, T.5    Niazi, F.6
  • 41
    • 84865790893 scopus 로고    scopus 로고
    • Acinetobacter, Aeromonas and Trichococcus populations dominate the microbial community within urban sewer infrastructure
    • VandeWalle JL, Goetz GW, Huse SM, Morrison HG, Sogin ML, Hoffmann RG et al. (2012). Acinetobacter, Aeromonas and Trichococcus populations dominate the microbial community within urban sewer infrastructure. Environ Microbiol 14: 2538-2552.
    • (2012) Environ Microbiol , vol.14 , pp. 2538-2552
    • Vandewalle, J.L.1    Goetz, G.W.2    Huse, S.M.3    Morrison, H.G.4    Sogin, M.L.5    Hoffmann, R.G.6
  • 43
    • 84865105014 scopus 로고    scopus 로고
    • DySC: Software for greedy clustering of 16S rRNA reads
    • Zheng ZJ, Kramer S, Schmidt B. (2012). DySC: software for greedy clustering of 16S rRNA reads. Bioinformatics 28: 2182-2183.
    • (2012) Bioinformatics , vol.28 , pp. 2182-2183
    • Zheng, Z.J.1    Kramer, S.2    Schmidt, B.3


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