Literature DB >> 19668203

Accurate determination of microbial diversity from 454 pyrosequencing data.

Christopher Quince1, Anders Lanzén, Thomas P Curtis, Russell J Davenport, Neil Hall, Ian M Head, L Fiona Read, William T Sloan.   

Abstract

We present an algorithm, PyroNoise, that clusters the flowgrams of 454 pyrosequencing reads using a distance measure that models sequencing noise. This infers the true sequences in a collection of amplicons. We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated.

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Year:  2009        PMID： 19668203     DOI： 10.1038/nmeth.1361

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  16 in total

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Journal:  Nucleic Acids Res       Date:  2004-03-19       Impact factor: 16.971

2.  Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness.

Authors:  Patrick D Schloss; Jo Handelsman
Journal:  Appl Environ Microbiol       Date:  2005-03       Impact factor: 4.792

3.  Microbial population structures in the deep marine biosphere.

Authors:  Julie A Huber; David B Mark Welch; Hilary G Morrison; Susan M Huse; Phillip R Neal; David A Butterfield; Mitchell L Sogin
Journal:  Science       Date:  2007-10-05       Impact factor: 47.728

4.  Pyrobayes: an improved base caller for SNP discovery in pyrosequences.

Authors:  Aaron R Quinlan; Donald A Stewart; Michael P Strömberg; Gábor T Marth
Journal:  Nat Methods       Date:  2008-01-13       Impact factor: 28.547

5.  The rational exploration of microbial diversity.

Authors:  Christopher Quince; Thomas P Curtis; William T Sloan
Journal:  ISME J       Date:  2008-07-24       Impact factor: 10.302

6.  The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species.

Authors:  G C Wang; Y Wang
Journal:  Microbiology (Reading)       Date:  1996-05       Impact factor: 2.777

7.  New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras.

Authors:  Kevin E Ashelford; Nadia A Chuzhanova; John C Fry; Antonia J Jones; Andrew J Weightman
Journal:  Appl Environ Microbiol       Date:  2006-09       Impact factor: 4.792

8.  UniFrac: a new phylogenetic method for comparing microbial communities.

Authors:  Catherine Lozupone; Rob Knight
Journal:  Appl Environ Microbiol       Date:  2005-12       Impact factor: 4.792

9.  MAFFT version 5: improvement in accuracy of multiple sequence alignment.

Authors:  Kazutaka Katoh; Kei-ichi Kuma; Hiroyuki Toh; Takashi Miyata
Journal:  Nucleic Acids Res       Date:  2005-01-20       Impact factor: 16.971

10.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.

Authors:  J R Cole; Q Wang; E Cardenas; J Fish; B Chai; R J Farris; A S Kulam-Syed-Mohideen; D M McGarrell; T Marsh; G M Garrity; J M Tiedje
Journal:  Nucleic Acids Res       Date:  2008-11-12       Impact factor: 16.971
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  423 in total

1.  Individual genome assembly from complex community short-read metagenomic datasets.

Authors:  Chengwei Luo; Despina Tsementzi; Nikos C Kyrpides; Konstantinos T Konstantinidis
Journal:  ISME J       Date:  2011-10-27       Impact factor: 10.302

2.  Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships.

Authors:  Jürg Brendan Logue; Silke Langenheder; Anders F Andersson; Stefan Bertilsson; Stina Drakare; Anders Lanzén; Eva S Lindström
Journal:  ISME J       Date:  2011-12-15       Impact factor: 10.302

3.  Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance.

Authors:  Johanna Sjöstedt; Per Koch-Schmidt; Mikael Pontarp; Björn Canbäck; Anders Tunlid; Per Lundberg; Ake Hagström; Lasse Riemann
Journal:  Appl Environ Microbiol       Date:  2011-12-22       Impact factor: 4.792

4.  Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome.

Authors:  David T Pride; Julia Salzman; Matthew Haynes; Forest Rohwer; Clara Davis-Long; Richard A White; Peter Loomer; Gary C Armitage; David A Relman
Journal:  ISME J       Date:  2011-12-08       Impact factor: 10.302

5.  DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences.

Authors:  Erik S Wright; L Safak Yilmaz; Daniel R Noguera
Journal:  Appl Environ Microbiol       Date:  2011-11-18       Impact factor: 4.792

6.  Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air.

Authors:  Naomichi Yamamoto; Kyle Bibby; Jing Qian; Denina Hospodsky; Hamid Rismani-Yazdi; William W Nazaroff; Jordan Peccia
Journal:  ISME J       Date:  2012-04-05       Impact factor: 10.302

7.  Comparative approach to capture bacterial diversity of coastal waters.

Authors:  Hyunsoo Na; Ok-Sun Kim; Seok-Hwan Yoon; Yunmin Kim; Jongsik Chun
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8.  Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.

Authors:  Jay McCarren; Jamie W Becker; Daniel J Repeta; Yanmei Shi; Curtis R Young; Rex R Malmstrom; Sallie W Chisholm; Edward F DeLong
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-31       Impact factor: 11.205

9.  Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.

Authors:  Migun Shakya; Christopher Quince; James H Campbell; Zamin K Yang; Christopher W Schadt; Mircea Podar
Journal:  Environ Microbiol       Date:  2013-02-06       Impact factor: 5.491

Review 10.  Advances in monitoring soil microbial community dynamic and function.

Authors:  K K Nkongolo; R Narendrula-Kotha
Journal:  J Appl Genet       Date:  2020-02-15       Impact factor: 3.240
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