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Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR, Cary SC.

PLoS One. 2012;7(9):e44224. doi: 10.1371/journal.pone.0044224. Epub 2012 Sep 6.


PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets.

Pinto AJ, Raskin L.

PLoS One. 2012;7(8):e43093. doi: 10.1371/journal.pone.0043093. Epub 2012 Aug 15.


Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure.

Huber JA, Morrison HG, Huse SM, Neal PR, Sogin ML, Mark Welch DB.

Environ Microbiol. 2009 May;11(5):1292-302. doi: 10.1111/j.1462-2920.2008.01857.x. Epub 2009 Feb 9.


Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

Schloss PD, Gevers D, Westcott SL.

PLoS One. 2011;6(12):e27310. doi: 10.1371/journal.pone.0027310. Epub 2011 Dec 14.


Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers.

Myer PR, Kim M, Freetly HC, Smith TP.

J Microbiol Methods. 2016 Aug;127:132-40. doi: 10.1016/j.mimet.2016.06.004. Epub 2016 Jun 6.


Removing noise from pyrosequenced amplicons.

Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ.

BMC Bioinformatics. 2011 Jan 28;12:38. doi: 10.1186/1471-2105-12-38.


Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities.

Bradley IM, Pinto AJ, Guest JS.

Appl Environ Microbiol. 2016 Sep 16;82(19):5878-91. doi: 10.1128/AEM.01630-16. Print 2016 Oct 1.


Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method.

Wu JY, Jiang XT, Jiang YX, Lu SY, Zou F, Zhou HW.

BMC Microbiol. 2010 Oct 12;10:255. doi: 10.1186/1471-2180-10-255.


A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.

de Muinck EJ, Trosvik P, Gilfillan GD, Hov JR, Sundaram AYM.

Microbiome. 2017 Jul 6;5(1):68. doi: 10.1186/s40168-017-0279-1.


Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.

Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG.

Environ Microbiol. 2014 Sep;16(9):2659-71. doi: 10.1111/1462-2920.12250. Epub 2013 Sep 18.


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

Sinclair L, Osman OA, Bertilsson S, Eiler A.

PLoS One. 2015 Feb 3;10(2):e0116955. doi: 10.1371/journal.pone.0116955. eCollection 2015.


The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

Ibarbalz FM, PĂ©rez MV, Figuerola EL, Erijman L.

PLoS One. 2014 Jun 12;9(6):e99722. doi: 10.1371/journal.pone.0099722. eCollection 2014.


Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets.

Yu G, Fadrosh D, Goedert JJ, Ravel J, Goldstein AM.

PLoS One. 2015 Jul 21;10(7):e0132253. doi: 10.1371/journal.pone.0132253. eCollection 2015.


Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys.

Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS.

Appl Environ Microbiol. 2009 Aug;75(16):5227-36. doi: 10.1128/AEM.00592-09. Epub 2009 Jun 26.


Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys.

Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J.

PLoS One. 2014 Apr 10;9(4):e94249. doi: 10.1371/journal.pone.0094249. eCollection 2014.


Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.

Ceuppens S, De Coninck D, Bottledoorn N, Van Nieuwerburgh F, Uyttendaele M.

Int J Food Microbiol. 2017 Sep 18;257:148-156. doi: 10.1016/j.ijfoodmicro.2017.06.016. Epub 2017 Jun 17.


Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions.

Behnke A, Engel M, Christen R, Nebel M, Klein RR, Stoeck T.

Environ Microbiol. 2011 Feb;13(2):340-9. doi: 10.1111/j.1462-2920.2010.02332.x. Epub 2010 Sep 8.


Distribution-based clustering: using ecology to refine the operational taxonomic unit.

Preheim SP, Perrotta AR, Martin-Platero AM, Gupta A, Alm EJ.

Appl Environ Microbiol. 2013 Nov;79(21):6593-603. doi: 10.1128/AEM.00342-13. Epub 2013 Aug 23.


Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.

Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, Sogin ML.

PLoS Genet. 2008 Nov;4(11):e1000255. doi: 10.1371/journal.pgen.1000255. Epub 2008 Nov 21. Erratum in: PLoS Genet. 2008 Dec;4(12). doi: 10.1371/annotation/3d8a6578-ce56-45aa-bc71-05078355b851. Welch, David Mark [corrected to Mark Welch, David].


Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform.

Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O'Donnell A.

J Microbiol Methods. 2012 Oct;91(1):80-8. doi: 10.1016/j.mimet.2012.07.008. Epub 2012 Jul 29.


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