Literature DB >> 21890669

Barcoded primers used in multiplex amplicon pyrosequencing bias amplification.

David Berry1, Karim Ben Mahfoudh, Michael Wagner, Alexander Loy.   

Abstract

"Barcode-tagged" PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

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Substances：

Year:  2011        PMID： 21890669      PMCID： PMC3209180          DOI： 10.1128/AEM.05220-11

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  20 in total

1.  Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

Authors:  Anthony S Amend; Keith A Seifert; Thomas D Bruns
Journal:  Mol Ecol       Date:  2010-11-03       Impact factor: 6.185

2.  Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.

Authors:  Brian J Haas; Dirk Gevers; Ashlee M Earl; Mike Feldgarden; Doyle V Ward; Georgia Giannoukos; Dawn Ciulla; Diana Tabbaa; Sarah K Highlander; Erica Sodergren; Barbara Methé; Todd Z DeSantis; Joseph F Petrosino; Rob Knight; Bruce W Birren
Journal:  Genome Res       Date:  2011-01-06       Impact factor: 9.043

3.  Parallel tagged sequencing on the 454 platform.

Authors:  Matthias Meyer; Udo Stenzel; Michael Hofreiter
Journal:  Nat Protoc       Date:  2008       Impact factor: 13.491

4.  Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

Authors:  Anna Engelbrektson; Victor Kunin; Kelly C Wrighton; Natasha Zvenigorodsky; Feng Chen; Howard Ochman; Philip Hugenholtz
Journal:  ISME J       Date:  2010-01-21       Impact factor: 10.302

5.  Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.

Authors:  Victor Kunin; Anna Engelbrektson; Howard Ochman; Philip Hugenholtz
Journal:  Environ Microbiol       Date:  2009-08-27       Impact factor: 5.491

6.  Reproducibility and quantitation of amplicon sequencing-based detection.

Authors:  Jizhong Zhou; Liyou Wu; Ye Deng; Xiaoyang Zhi; Yi-Huei Jiang; Qichao Tu; Jianping Xie; Joy D Van Nostrand; Zhili He; Yunfeng Yang
Journal:  ISME J       Date:  2011-02-24       Impact factor: 10.302

7.  Ironing out the wrinkles in the rare biosphere through improved OTU clustering.

Authors:  Susan M Huse; David Mark Welch; Hilary G Morrison; Mitchell L Sogin
Journal:  Environ Microbiol       Date:  2010-03-11       Impact factor: 5.491

8.  The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies.

Authors:  Patrick D Schloss
Journal:  PLoS Comput Biol       Date:  2010-07-08       Impact factor: 4.475

9.  QIIME allows analysis of high-throughput community sequencing data.

Authors:  J Gregory Caporaso; Justin Kuczynski; Jesse Stombaugh; Kyle Bittinger; Frederic D Bushman; Elizabeth K Costello; Noah Fierer; Antonio Gonzalez Peña; Julia K Goodrich; Jeffrey I Gordon; Gavin A Huttley; Scott T Kelley; Dan Knights; Jeremy E Koenig; Ruth E Ley; Catherine A Lozupone; Daniel McDonald; Brian D Muegge; Meg Pirrung; Jens Reeder; Joel R Sevinsky; Peter J Turnbaugh; William A Walters; Jeremy Widmann; Tanya Yatsunenko; Jesse Zaneveld; Rob Knight
Journal:  Nat Methods       Date:  2010-04-11       Impact factor: 28.547

10.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.

Authors:  Elmar Pruesse; Christian Quast; Katrin Knittel; Bernhard M Fuchs; Wolfgang Ludwig; Jörg Peplies; Frank Oliver Glöckner
Journal:  Nucleic Acids Res       Date:  2007-10-18       Impact factor: 16.971
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  171 in total

1.  Actinobacterial nitrate reducers and proteobacterial denitrifiers are abundant in N2O-metabolizing palsa peat.

Authors:  Katharina Palmer; Marcus A Horn
Journal:  Appl Environ Microbiol       Date:  2012-06-01       Impact factor: 4.792

2.  Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability.

Authors:  Kathleen M Morrow; Anthony G Moss; Nanette E Chadwick; Mark R Liles
Journal:  Appl Environ Microbiol       Date:  2012-07-06       Impact factor: 4.792

3.  Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape.

Authors:  K Lothamer; S P Brown; J D Mattox; A Jumpponen
Journal:  Mycorrhiza       Date:  2013-11-13       Impact factor: 3.387

4.  Communities of ammonia oxidizers at different stages of Spartina alterniflora invasion in salt marshes of Yangtze River estuary.

Authors:  Fei Xia; Jemaneh Zeleke; Qiang Sheng; Ji-Hua Wu; Zhe-Xue Quan
Journal:  J Microbiol       Date:  2015-05-03       Impact factor: 3.422

5.  Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms.

Authors:  Linda Wilhelm; Katharina Besemer; Lena Fragner; Hannes Peter; Wolfram Weckwerth; Tom J Battin
Journal:  ISME J       Date:  2015-05-15       Impact factor: 10.302

6.  NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds.

Authors:  J Diaz-Real; D Serrano; A Piriz; R Jovani
Journal:  Exp Appl Acarol       Date:  2015-07-03       Impact factor: 2.132

7.  Residual soil DNA extraction increases the discriminatory power between samples.

Authors:  Jennifer M Young; Laura S Weyrich; Laurence J Clarke; Alan Cooper
Journal:  Forensic Sci Med Pathol       Date:  2015-02-27       Impact factor: 2.007

8.  Impact of long-term diesel contamination on soil microbial community structure.

Authors:  Nora B Sutton; Farai Maphosa; Jose A Morillo; Waleed Abu Al-Soud; Alette A M Langenhoff; Tim Grotenhuis; Huub H M Rijnaarts; Hauke Smidt
Journal:  Appl Environ Microbiol       Date:  2012-11-09       Impact factor: 4.792

9.  Methyl coenzyme M reductase A (mcrA) gene-based investigation of methanogens in the mudflat sediments of Yangtze River estuary, China.

Authors:  Jemaneh Zeleke; Shui-Long Lu; Jian-Gong Wang; Jing-Xin Huang; Bo Li; Andrew V Ogram; Zhe-Xue Quan
Journal:  Microb Ecol       Date:  2013-01-11       Impact factor: 4.552

10.  Polycyclic aromatic hydrocarbon degradation of phytoplankton-associated Arenibacter spp. and description of Arenibacter algicola sp. nov., an aromatic hydrocarbon-degrading bacterium.

Authors:  Tony Gutierrez; Glenn Rhodes; Sara Mishamandani; David Berry; William B Whitman; Peter D Nichols; Kirk T Semple; Michael D Aitken
Journal:  Appl Environ Microbiol       Date:  2013-11-08       Impact factor: 4.792
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