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Volumn 10, Issue 2, 2015, Pages

Microbial community composition and diversity via 16S rRNA gene amplicons: Evaluating the illumina platform

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL DNA;

EID: 84922385648     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0116955     Document Type: Article
Times cited : (286)

References (48)
  • 2
    • 0030661563 scopus 로고    scopus 로고
    • Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16s rrna
    • PMID: 9361437
    • Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology 63: 4516-4522. PMID: 9361437
    • (1997) Applied and Environmental Microbiology , vol.63 , pp. 4516-4522
    • Liu, W.T.1    Marsh, T.L.2    Cheng, H.3    Forney, L.J.4
  • 3
    • 0032879764 scopus 로고    scopus 로고
    • Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities
    • PMID: 10508099
    • Fisher MM, Triplett EW (1999) Automated Approach for Ribosomal Intergenic Spacer Analysis of Microbial Diversity and Its Application to Freshwater Bacterial Communities. Applied and Environmental Microbiology 65: 4630-4636. PMID: 10508099
    • (1999) Applied and Environmental Microbiology , vol.65 , pp. 4630-4636
    • Fisher, M.M.1    Triplett, E.W.2
  • 5
    • 50949131523 scopus 로고    scopus 로고
    • Comparative analysis of human gut microbiota by barcoded pyrosequencing
    • PMID: 18665274
    • Andersson AF, Andersson AF, Lindberg M, Lindberg M, Jakobsson H, et al. (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3: e2836. doi: 10.1371/journal. pone.0002836 PMID: 18665274
    • (2008) PLoS ONE , vol.3
    • Andersson, A.F.1    Andersson, A.F.2    Lindberg, M.3    Lindberg, M.4    Jakobsson, H.5
  • 6
    • 40149103278 scopus 로고    scopus 로고
    • Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
    • PMID: 18264105
    • Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods 5: 235-237. doi: 10.1038/nmeth.1184 PMID: 18264105
    • (2008) Nature Methods , vol.5 , pp. 235-237
    • Hamady, M.1    Walker, J.J.2    Harris, J.K.3    Gold, N.J.4    Knight, R.5
  • 8
    • 80052964484 scopus 로고    scopus 로고
    • Transitions in bacterial communities along the 2000km salinity gradient of the baltic sea
    • PMID: 21472016
    • Herlemann DP, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, et al. (2011) Transitions in bacterial communities along the 2000km salinity gradient of the Baltic Sea. The ISME Journal 5: 1571-1579. doi: 10.1038/ismej.2011.41 PMID: 21472016
    • (2011) The ISME Journal , vol.5 , pp. 1571-1579
    • Herlemann, D.P.1    Labrenz, M.2    Jürgens, K.3    Bertilsson, S.4    Waniek, J.J.5
  • 9
    • 84855951093 scopus 로고    scopus 로고
    • Coherent dynamics and association networks among lake bacterioplankton taxa
    • PMID: 21881616
    • Eiler A, Heinrich F, Bertilsson S (2011) Coherent dynamics and association networks among lake bacterioplankton taxa. The ISME Journal 6: 330-342. doi: 10.1038/ismej.2011.113 PMID: 21881616
    • (2011) The ISME Journal , vol.6 , pp. 330-342
    • Eiler, A.1    Heinrich, F.2    Bertilsson, S.3
  • 10
    • 69549112742 scopus 로고    scopus 로고
    • Accurate determination of microbial diversity from 454 pyrosequencing data
    • PMID: 19668203
    • Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 6: 639-641. doi: 10.1038/nmeth.1361 PMID: 19668203
    • (2009) Nature Methods , vol.6 , pp. 639-641
    • Quince, C.1    Lanzén, A.2    Curtis, T.P.3    Davenport, R.J.4    Hall, N.5
  • 11
    • 69549129476 scopus 로고    scopus 로고
    • The 'rare biosphere': A reality check
    • PMID: 19718016
    • Reeder J, Knight R (2009) The 'rare biosphere': a reality check. Nature Methods 6: 636-637. doi: 10. 1038/nmeth0909-636 PMID: 19718016
    • (2009) Nature Methods , vol.6 , pp. 636-637
    • Reeder, J.1    Knight, R.2
  • 13
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved otu clustering
    • PMID: 20236171
    • Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology 12: 1889-1898. doi: 10.1111/j.1462- 2920.2010.02193.x PMID: 20236171
    • (2010) Environmental Microbiology , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 14
    • 77951498638 scopus 로고    scopus 로고
    • Experimental factors affecting pcr-based estimates of microbial species richness and evenness
    • PMID: 20090784
    • Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, et al. (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. The ISME Journal 4: 642-647. doi: 10.1038/ismej.2009.153 PMID: 20090784
    • (2010) The ISME Journal , vol.4 , pp. 642-647
    • Engelbrektson, A.1    Kunin, V.2    Wrighton, K.C.3    Zvenigorodsky, N.4    Chen, F.5
  • 15
    • 77956283658 scopus 로고    scopus 로고
    • 454 pyrosequencing and sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
    • PMID: 20636324
    • Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, et al. (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. The New phytologist 188: 291-301. doi: 10.1111/j.1469-8137.2010.03373.x PMID: 20636324
    • (2010) The New Phytologist , vol.188 , pp. 291-301
    • Tedersoo, L.1    Nilsson, R.H.2    Abarenkov, K.3    Jairus, T.4    Sadam, A.5
  • 16
    • 84884904719 scopus 로고    scopus 로고
    • UPARSE: Highly accurate otu sequences from microbial amplicon reads
    • PMID: 23955772
    • Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10: 996-998. doi: 10.1038/nmeth.2604 PMID: 23955772
    • (2013) Nature Methods , vol.10 , pp. 996-998
    • Edgar, R.C.1
  • 17
    • 78650453707 scopus 로고    scopus 로고
    • Comparison of two nextgeneration sequencing technologies for resolving highly complex microbiota composition using tandem variable 16s rrna gene regions
    • PMID: 20880993
    • Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, et al. (2010) Comparison of two nextgeneration sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Research 38: e200-e200. doi: 10.1093/nar/gkq873 PMID: 20880993
    • (2010) Nucleic Acids Research , vol.38 , pp. e200-e200
    • Claesson, M.J.1    Wang, Q.2    O'Sullivan, O.3    Greene-Diniz, R.4    Cole, J.R.5
  • 18
    • 79961081161 scopus 로고    scopus 로고
    • Generation of multimillion- sequence 16s rrna gene libraries from complex microbial communities by assembling paired-end illumina reads
    • PMID: 21460107
    • Bartram AK, Lynch MDJ, Stearns JC, Moreno-Hagelsieb G, Neufeld JD (2011) Generation of multimillion- sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Applied and Environmental Microbiology 77: 3846-3852. doi: 10.1128/AEM.02772-10 PMID: 21460107
    • (2011) Applied and Environmental Microbiology , vol.77 , pp. 3846-3852
    • Bartram, A.K.1    Lynch, M.D.J.2    Stearns, J.C.3    Moreno-Hagelsieb, G.4    Neufeld, J.D.5
  • 19
    • 84355163066 scopus 로고    scopus 로고
    • Illumina-based analysis of microbial community diversity
    • PMID: 21677692
    • Degnan PH, Ochman H (2011) Illumina-based analysis of microbial community diversity. The ISME Journal 6: 183-194. doi: 10.1038/ismej.2011.74 PMID: 21677692
    • (2011) The ISME Journal , vol.6 , pp. 183-194
    • Degnan, P.H.1    Ochman, H.2
  • 20
    • 78149429458 scopus 로고    scopus 로고
    • Microbiome profiling by illumina sequencing of combinatorial sequence-tagged pcr products
    • PMID: 21048977
    • Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, et al. (2010) Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products. PLoS ONE 5: e15406. doi: 10.1371/journal.pone.0015406 PMID: 21048977
    • (2010) PLoS ONE , vol.5
    • Gloor, G.B.1    Hummelen, R.2    Macklaim, J.M.3    Dickson, R.J.4    Fernandes, A.D.5
  • 21
    • 84863981120 scopus 로고    scopus 로고
    • Ultra-high-throughput microbial community analysis on the illumina hiseq and miseq platforms
    • PMID: 22402401
    • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal 6: 1621-1624. doi: 10.1038/ismej.2012.8 PMID: 22402401
    • (2012) The ISME Journal , vol.6 , pp. 1621-1624
    • Caporaso, J.G.1    Lauber, C.L.2    Walters, W.A.3    Berg-Lyons, D.4    Huntley, J.5
  • 22
    • 79953026036 scopus 로고    scopus 로고
    • BIPES, a cost-effective high-throughput method for assessing microbial diversity
    • PMID: 20962877
    • Zhou HW, Li DF, Tam NFY, Jiang XT, Zhang H, et al. (2010) BIPES, a cost-effective high-throughput method for assessing microbial diversity. The ISME Journal 5: 741-749. doi: 10.1038/ismej.2010.160 PMID: 20962877
    • (2010) The ISME Journal , vol.5 , pp. 741-749
    • Zhou, H.W.1    Li, D.F.2    Tam, N.F.Y.3    Jiang, X.T.4    Zhang, H.5
  • 23
    • 84884251320 scopus 로고    scopus 로고
    • Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform
    • PMID: 23793624
    • Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology 79: 5112-5120. doi: 10.1128/AEM. 01043-13 PMID: 23793624
    • (2013) Applied and Environmental Microbiology , vol.79 , pp. 5112-5120
    • Kozich, J.J.1    Westcott, S.L.2    Baxter, N.T.3    Highlander, S.K.4    Schloss, P.D.5
  • 24
    • 84860756398 scopus 로고    scopus 로고
    • Performance comparison of benchtop high-throughput sequencing platforms
    • PMID: 22522955
    • Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, et al. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology 30: 434-439. doi: 10. 1038/nbt.2198 PMID: 22522955
    • (2012) Nature Biotechnology , vol.30 , pp. 434-439
    • Loman, N.J.1    Misra, R.V.2    Dallman, T.J.3    Constantinidou, C.4    Gharbia, S.E.5
  • 25
    • 84901692841 scopus 로고    scopus 로고
    • Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change
    • PMID: 24597511
    • Osman OA, Gudasz C, Bertilsson S (2014) Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change. FEMS Microbiology Ecology 88: 468-481. doi: 10. 1111/1574-6941.12312 PMID: 24597511
    • (2014) FEMS Microbiology Ecology , vol.88 , pp. 468-481
    • Osman, O.A.1    Gudasz, C.2    Bertilsson, S.3
  • 26
    • 84872132821 scopus 로고    scopus 로고
    • Taxonomic classification of bacterial 16s rrna genes using short sequencing reads: Evaluation of effective study designs
    • PMID: 23308262
    • Mizrahi-Man O, Davenport ER, Gilad Y (2013) Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs. PLoS ONE 8: e53608. doi: 10. 1371/journal.pone.0053608 PMID: 23308262
    • (2013) PLoS ONE , vol.8
    • Mizrahi-Man, O.1    Davenport, E.R.2    Gilad, Y.3
  • 27
    • 84872777339 scopus 로고    scopus 로고
    • Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach
    • PMID: 23349714
    • Eiler A, Drakare S, Bertilsson S, Pernthaler J, Peura S, et al. (2013) Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach. PLoS ONE 8: e53516. doi: 10.1371/journal.pone.0053516 PMID: 23349714
    • (2013) PLoS ONE , vol.8
    • Eiler, A.1    Drakare, S.2    Bertilsson, S.3    Pernthaler, J.4    Peura, S.5
  • 31
    • 79961181125 scopus 로고    scopus 로고
    • UCHIME improves sensitivity and speed of chimera detection
    • PMID: 21700674
    • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200. doi: 10.1093/bioinformatics/btr381 PMID: 21700674
    • (2011) Bioinformatics , vol.27 , pp. 2194-2200
    • Edgar, R.C.1    Haas, B.J.2    Clemente, J.C.3    Quince, C.4    Knight, R.5
  • 32
    • 84870027011 scopus 로고    scopus 로고
    • Ultrafast clustering algorithms for metagenomic sequence analysis
    • PMID: 22772836
    • Li W, Fu L, Niu B, Wu S, Wooley J (2012) Ultrafast clustering algorithms for metagenomic sequence analysis. Briefings in Bioinformatics 13: 656-668. doi: 10.1093/bib/bbs035 PMID: 22772836
    • (2012) Briefings in Bioinformatics , vol.13 , pp. 656-668
    • Li, W.1    Fu, L.2    Niu, B.3    Wu, S.4    Wooley, J.5
  • 33
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than blast
    • PMID: 20709691
    • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. doi: 10.1093/bioinformatics/btq461 PMID: 20709691
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 34
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high- throughput community sequencing data
    • PMID: 20383131
    • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high- throughput community sequencing data. Nature Methods 7: 335-336. doi: 10.1038/nmeth.f. 303 PMID: 20383131
    • (2010) Nature Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1    Kuczynski, J.2    Stombaugh, J.3    Bittinger, K.4    Bushman, F.D.5
  • 37
    • 84869030635 scopus 로고    scopus 로고
    • CREST - Classification resources for environmental sequence tags
    • PMID: 23145153
    • Lanzén A, Jørgensen SL, Huson DH, Gorfer M, Grindhaug SH, et al. (2012) CREST - Classification Resources for Environmental Sequence Tags. PLoS ONE 7: e49334. doi: 10.1371/journal.pone. 0049334 PMID: 23145153
    • (2012) PLoS ONE , vol.7
    • Lanzén, A.1    Jørgensen, S.L.2    Huson, D.H.3    Gorfer, M.4    Grindhaug, S.H.5
  • 38
    • 84873739311 scopus 로고    scopus 로고
    • The silva ribosomal rna gene database project: Improved data processing and web-based tools
    • PMID: 23193283
    • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41: D590-6. doi: 10.1093/nar/gks1219 PMID: 23193283
    • (2013) Nucleic Acids Research , vol.41 , pp. D590-D596
    • Quast, C.1    Pruesse, E.2    Yilmaz, P.3    Gerken, J.4    Schweer, T.5
  • 39
    • 34548293679 scopus 로고    scopus 로고
    • Naive bayesian classifier for rapid assignment of rrna sequences into the new bacterial taxonomy
    • PMID: 17586664
    • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Applied and Environmental Microbiology 73: 5261-5267. PMID: 17586664
    • (2007) Applied and Environmental Microbiology , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 41
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: A new phylogenetic method for comparing microbial communities
    • PMID: 16332807
    • Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71: 8228-8235. PMID: 16332807
    • (2005) Applied and Environmental Microbiology , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 42
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: Opensource, platform-independent, community-supported software for describing and comparing microbial communities
    • PMID: 19801464
    • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: opensource, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541. doi: 10.1128/AEM.01541-09 PMID: 19801464
    • (2009) Applied and Environmental Microbiology , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3    Hall, J.R.4    Hartmann, M.5
  • 43
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • PMID: 20224823
    • Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490. doi: 10.1371/journal.pone.0009490 PMID: 20224823
    • (2010) PLoS ONE , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 45
    • 84865319078 scopus 로고    scopus 로고
    • Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division od1
    • Peura S, Eiler A, Bertilsson S, Nykänen H, Tiirola M, et al. (2012) Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1. The ISME Journal: 1-13.
    • (2012) The ISME Journal , pp. 1-13
    • Peura, S.1    Eiler, A.2    Bertilsson, S.3    Nykänen, H.4    Tiirola, M.5
  • 46
    • 76349119916 scopus 로고    scopus 로고
    • Pyrosequencing reveals contrasting seasonal dynamics of taxa within baltic sea bacterioplankton communities
    • PMID: 19829318
    • Andersson AF, Riemann L, Bertilsson S (2009) Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities. The ISME Journal 4: 171-181. doi: 10. 1038/ismej.2009.108 PMID: 19829318
    • (2009) The ISME Journal , vol.4 , pp. 171-181
    • Andersson, A.F.1    Riemann, L.2    Bertilsson, S.3
  • 47
    • 84899679811 scopus 로고    scopus 로고
    • Systematic design of 18s rrna gene primers for determining eukaryotic diversity in microbial consortia
    • PMID: 24755918
    • Hugerth LW, Muller EEL, Hu YOO, Lebrun LAM, Roume H, et al. (2014) Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia. PLoS ONE 9: e95567. doi: 10.1371/journal.pone.0095567 PMID: 24755918
    • (2014) PLoS ONE , vol.9
    • Hugerth, L.W.1    Muller, E.E.L.2    Hu, Y.O.O.3    Lebrun, L.A.M.4    Roume, H.5
  • 48
    • 45549097485 scopus 로고    scopus 로고
    • Spatial scaling of functional gene diversity across various microbial taxa
    • PMID: 18509054
    • Zhou J, Kang S, Schadt CW, Garten CT (2008) Spatial scaling of functional gene diversity across various microbial taxa. PNAS 105: 7768-7773. doi: 10.1073/pnas.0709016105 PMID: 18509054
    • (2008) PNAS , vol.105 , pp. 7768-7773
    • Zhou, J.1    Kang, S.2    Schadt, C.W.3    Garten, C.T.4


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