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Volumn 17, Issue 1, 2016, Pages

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; RNA 16S;

EID: 84954357595     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2194-9     Document Type: Article
Times cited : (299)

References (40)
  • 1
    • 84866887118 scopus 로고    scopus 로고
    • Large variations in bacterial ribosomal RNA genes
    • Lim K, Furuta Y, Kobayashi I. Large variations in bacterial ribosomal RNA genes. Mol Biol Evol. 2012; 29(10):2937-48.
    • (2012) Mol Biol Evol , vol.29 , Issue.10 , pp. 2937-2948
    • Lim, K.1    Furuta, Y.2    Kobayashi, I.3
  • 3
    • 0029789623 scopus 로고    scopus 로고
    • A quantitative map of nucleotide substitution rates in bacterial rRNA
    • Van de Peer Y, Chapelle S, De Wachter R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucl Acids Res. 1996; 24:3381-91.
    • (1996) Nucl Acids Res , vol.24 , pp. 3381-3391
    • Van de Peer, Y.1    Chapelle, S.2
  • 4
    • 84878666389 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, Pelies J, Quast C, Horn M, et al.Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2012; 20:1-11.
    • (2012) Nucleic Acids Res , vol.20 , pp. 1-11
    • Klindworth, A.1    Pruesse, E.2    Schweer, T.3    Pelies, J.4    Quast, C.5    Horn, M.6
  • 5
    • 84892488033 scopus 로고    scopus 로고
    • The effect of primer choice and short read sequences on the outcom of 16S rRNA gene based diversity studies
    • Ghyselinck J, Pfeiffer S, Heylen K, Sessitsch A, De Vos P. The effect of primer choice and short read sequences on the outcom of 16S rRNA gene based diversity studies. PLoS One. 2013; 8(8):e71360.
    • (2013) PLoS One , vol.8 , Issue.8
    • Ghyselinck, J.1    Pfeiffer, S.2    Heylen, K.3    Sessitsch, A.4    De Vos, P.5
  • 6
    • 84865060813 scopus 로고    scopus 로고
    • PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets
    • Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One. 2012; 7(8):e43093.
    • (2012) PLoS One , vol.7 , Issue.8
    • Pinto, A.J.1    Raskin, L.2
  • 7
    • 84862631902 scopus 로고    scopus 로고
    • Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
    • Soergel DAW, Dey N, Knight R, Brenner SE. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J. 2012; 6:1440-4.
    • (2012) ISME J , vol.6 , pp. 1440-1444
    • Soergel, D.A.W.1    Dey, N.2    Knight, R.3    Brenner, S.E.4
  • 9
    • 84920629237 scopus 로고    scopus 로고
    • A renaissance for the pioneering 16S rRNA gene
    • Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol. 2008; 11:442-6.
    • (2008) Curr Opin Microbiol , vol.11 , pp. 442-446
    • Tringe, S.G.1    Hugenholtz, P.2
  • 12
    • 77956304094 scopus 로고    scopus 로고
    • Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
    • Reeder J, Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods. 2010; 7:668-9.
    • (2010) Nat Methods , vol.7 , pp. 668-669
    • Reeder, J.1    Knight, R.2
  • 13
    • 35549007148 scopus 로고    scopus 로고
    • Short pyrosequencing reads suffice for accurate microbial community analysis
    • Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucl Acids Res. 2007; 35(18):e120.
    • (2007) Nucl Acids Res , vol.35 , Issue.18
    • Liu, Z.1    Lozupone, C.2    Hamady, M.3    Bushman, F.D.4    Knight, R.5
  • 14
    • 84862620989 scopus 로고    scopus 로고
    • Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys
    • Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J. 2012; 6(7):1273-6.
    • (2012) ISME J , vol.6 , Issue.7 , pp. 1273-1276
    • Werner, J.J.1    Zhou, D.2    Caporaso, J.G.3    Knight, R.4    Angenent, L.T.5
  • 15
    • 84893723345 scopus 로고    scopus 로고
    • Library preparation methods for next-generation sequencing: tone down the bias
    • van Dijk EL, Jaszczyszyn Y, Thermes C. Library preparation methods for next-generation sequencing: tone down the bias. Exp Cell Res. 2014; 322(1):12-20.
    • (2014) Exp Cell Res , vol.322 , Issue.1 , pp. 12-20
    • van Dijk, E.L.1    Jaszczyszyn, Y.2    Thermes, C.3
  • 16
    • 78650568308 scopus 로고    scopus 로고
    • SAMStat: monitoring biases in next generation sequencing data
    • Lassmann T, Hayashizaki Y, Daub CO. SAMStat: monitoring biases in next generation sequencing data. Bioinformatics. 2011; 27(1):130-1.
    • (2011) Bioinformatics , vol.27 , Issue.1 , pp. 130-131
    • Lassmann, T.1    Hayashizaki, Y.2    Daub, C.O.3
  • 17
    • 84906567656 scopus 로고    scopus 로고
    • Microbiology: Microbiome science needs a healthy dose of scepticism
    • Hanage WP. Microbiology: Microbiome science needs a healthy dose of scepticism. Nature. 2014; 512(7514):247-8.
    • (2014) Nature , vol.512 , Issue.7514 , pp. 247-248
    • Hanage, W.P.1
  • 20
    • 84875389052 scopus 로고    scopus 로고
    • Considerations for the development and application of control materials to improve metagenomic microbial community profiling
    • Huggett JF, Laver T, Tamisak S, Nixon G, O'Sullivan DM, Elaswarapu R, et al.Considerations for the development and application of control materials to improve metagenomic microbial community profiling. Accred Qual Assur. 2013; 18(2):77-83.
    • (2013) Accred Qual Assur , vol.18 , Issue.2 , pp. 77-83
    • Huggett, J.F.1    Laver, T.2    Tamisak, S.3    Nixon, G.4    O'Sullivan, D.M.5    Elaswarapu, R.6
  • 21
    • 75549083380 scopus 로고    scopus 로고
    • Reducing the impact of pcr-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity dna polymerase
    • Lahr DJ, Katz LA. Reducing the impact of pcr-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity dna polymerase. Biotechniques. 2009; 47(4):857-66.
    • (2009) Biotechniques , vol.47 , Issue.4 , pp. 857-866
    • Lahr, D.J.1    Katz, L.A.2
  • 22
    • 34547834963 scopus 로고    scopus 로고
    • The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
    • Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, Nielsen R, et al.The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE. 2007; 2(2):e197.
    • (2007) PLoS ONE , vol.2 , Issue.2
    • Binladen, J.1    Gilbert, M.T.P.2    Bollback, J.P.3    Panitz, F.4    Bendixen, C.5    Nielsen, R.6
  • 23
    • 33846096244 scopus 로고    scopus 로고
    • Gene capture and random amplification for quantitative recovery of homologous genes
    • Crosby LD, Criddle CS. Gene capture and random amplification for quantitative recovery of homologous genes. Mol Cell Probes. 2007; 21(2):140-7.
    • (2007) Mol Cell Probes , vol.21 , Issue.2 , pp. 140-147
    • Crosby, L.D.1    Criddle, C.S.2
  • 24
    • 34548588390 scopus 로고    scopus 로고
    • Targeted high-throughput sequencing of tagged nucleic acid samples
    • Meyer M, Stenzel U, Myles S, Prufer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res. 2007; 35(15):e97.
    • (2007) Nucleic Acids Res , vol.35 , Issue.15 , pp. e97
    • Meyer, M.1    Stenzel, U.2    Myles, S.3    Prufer, K.4    Hofreiter, M.5
  • 25
    • 39449089394 scopus 로고    scopus 로고
    • Parallel tagged sequencing on the 454 platform
    • Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat Protoc. 2008; 3(2):267-78.
    • (2008) Nat Protoc , vol.3 , Issue.2 , pp. 267-278
    • Meyer, M.1    Stenzel, U.2    Hofreiter, M.3
  • 26
    • 72549096279 scopus 로고    scopus 로고
    • Depauperate genetic variability detected in the American and European bison using genomic techniques
    • Pertoldi C, Tokarska M, Wojcik JM, Demontis D, Loeschcke V, Gregersen VR, et al.Depauperate genetic variability detected in the American and European bison using genomic techniques. Biol Direct. 2009; 4:48.
    • (2009) Biol Direct , vol.4 , pp. 48
    • Pertoldi, C.1    Tokarska, M.2    Wojcik, J.M.3    Demontis, D.4    Loeschcke, V.5    Gregersen, V.R.6
  • 28
    • 84878647680 scopus 로고    scopus 로고
    • Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
    • Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol. 2013; 15(6):1882-99.
    • (2013) Environ Microbiol , vol.15 , Issue.6 , pp. 1882-1899
    • Shakya, M.1    Quince, C.2    Campbell, J.H.3    Yang, Z.K.4    Schadt, C.W.5    Podar, M.6
  • 29
    • 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.Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012; 6(8):1621-4.
    • (2012) ISME J , vol.6 , Issue.8 , 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
  • 31
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler Transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009; 25:1754-60.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 33
    • 84863229597 scopus 로고    scopus 로고
    • VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
    • Koboldt D, Zhang Q, Larson D, Shen D, McLellan M, Lin L, et al.VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012; 22(3):568-76.
    • (2012) Genome Res , vol.22 , Issue.3 , pp. 568-576
    • Koboldt, D.1    Zhang, Q.2    Larson, D.3    Shen, D.4    McLellan, M.5    Lin, L.6
  • 35
    • 84934769334 scopus 로고    scopus 로고
    • Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
    • Schirmer M, Ijaz UZ, D'Amore R, Hall N, Quince C. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 2015; 43(6):e37.
    • (2015) Nucleic Acids Res , vol.43 , Issue.6
    • Schirmer, M.1    Ijaz, U.Z.2    D'Amore, R.3    Hall, N.4    Quince, C.5
  • 36
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than blast
    • Edgar RC. Search and clustering orders of magnitude faster than blast. Bioinformatics. 2010; 26:2460-1.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 37
    • 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. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb. 2007; 73(16):5261-7.
    • (2007) Appl Environ Microb , vol.73 , Issue.16 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 38
    • 84855295457 scopus 로고    scopus 로고
    • Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
    • Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 2012; 40:e3.
    • (2012) Nucleic Acids Res , vol.40
    • Kircher, M.1    Sawyer, S.2    Meyer, M.3
  • 39
    • 84899531657 scopus 로고    scopus 로고
    • Analysis, optimization and verification of illumina-generated 16s rrna gene amplicon surveys
    • Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. Analysis, optimization and verification of illumina-generated 16s rrna gene amplicon surveys. PLoS ONE. 2014; 9(4):e94249.
    • (2014) PLoS ONE , vol.9 , Issue.4
    • Nelson, M.C.1    Morrison, H.G.2    Benjamino, J.3    Grim, S.L.4    Graf, J.5


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