Literature DB >> 23184592

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Justin Kuczynski1, Jesse Stombaugh, William Anton Walters, Antonio González, J Gregory Caporaso, Rob Knight.   

Abstract

QIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities.
© 2012 by John Wiley & Sons, Inc.

Entities:  

Mesh：

Substances：

Year:  2012        PMID： 23184592      PMCID： PMC4477843          DOI： 10.1002/9780471729259.mc01e05s27

Source DB:  PubMed          Journal:  Curr Protoc Microbiol        ISSN： 1934-8525


  9 in total

1.  New Generations: Sequencing Machines and Their Computational Challenges.

Authors:  David C Schwartz; Michael S Waterman
Journal:  J Comput Sci Technol       Date:  2010-01-01       Impact factor: 1.571

2.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Authors:  J Gregory Caporaso; Christian L Lauber; William A Walters; Donna Berg-Lyons; Catherine A Lozupone; Peter J Turnbaugh; Noah Fierer; Rob Knight
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-03       Impact factor: 11.205

3.  Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

Authors:  Qiong Wang; George M Garrity; James M Tiedje; James R Cole
Journal:  Appl Environ Microbiol       Date:  2007-06-22       Impact factor: 4.792

4.  Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation.

Authors:  Peter A Crawford; Jan R Crowley; Nandakumar Sambandam; Brian D Muegge; Elizabeth K Costello; Micah Hamady; Rob Knight; Jeffrey I Gordon
Journal:  Proc Natl Acad Sci U S A       Date:  2009-06-22       Impact factor: 11.205

5.  FastTree 2--approximately maximum-likelihood trees for large alignments.

Authors:  Morgan N Price; Paramvir S Dehal; Adam P Arkin
Journal:  PLoS One       Date:  2010-03-10       Impact factor: 3.240

6.  Enterotypes of the human gut microbiome.

Authors:  Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R Mende; Gabriel R Fernandes; Julien Tap; Thomas Bruls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; Francesc Casellas; Leyden Fernandez; Laurent Gautier; Torben Hansen; Masahira Hattori; Tetsuya Hayashi; Michiel Kleerebezem; Ken Kurokawa; Marion Leclerc; Florence Levenez; Chaysavanh Manichanh; H Bjørn Nielsen; Trine Nielsen; Nicolas Pons; Julie Poulain; Junjie Qin; Thomas Sicheritz-Ponten; Sebastian Tims; David Torrents; Edgardo Ugarte; Erwin G Zoetendal; Jun Wang; Francisco Guarner; Oluf Pedersen; Willem M de Vos; Søren Brunak; Joel Doré; María Antolín; François Artiguenave; Hervé M Blottiere; Mathieu Almeida; Christian Brechot; Carlos Cara; Christian Chervaux; Antonella Cultrone; Christine Delorme; Gérard Denariaz; Rozenn Dervyn; Konrad U Foerstner; Carsten Friss; Maarten van de Guchte; Eric Guedon; Florence Haimet; Wolfgang Huber; Johan van Hylckama-Vlieg; Alexandre Jamet; Catherine Juste; Ghalia Kaci; Jan Knol; Omar Lakhdari; Severine Layec; Karine Le Roux; Emmanuelle Maguin; Alexandre Mérieux; Raquel Melo Minardi; Christine M'rini; Jean Muller; Raish Oozeer; Julian Parkhill; Pierre Renault; Maria Rescigno; Nicolas Sanchez; Shinichi Sunagawa; Antonio Torrejon; Keith Turner; Gaetana Vandemeulebrouck; Encarna Varela; Yohanan Winogradsky; Georg Zeller; Jean Weissenbach; S Dusko Ehrlich; Peer Bork
Journal:  Nature       Date:  2011-04-20       Impact factor: 49.962

7.  PyNAST: a flexible tool for aligning sequences to a template alignment.

Authors:  J Gregory Caporaso; Kyle Bittinger; Frederic D Bushman; Todd Z DeSantis; Gary L Andersen; Rob Knight
Journal:  Bioinformatics       Date:  2009-11-13       Impact factor: 6.937

8.  A large genome center's improvements to the Illumina sequencing system.

Authors:  Michael A Quail; Iwanka Kozarewa; Frances Smith; Aylwyn Scally; Philip J Stephens; Richard Durbin; Harold Swerdlow; Daniel J Turner
Journal:  Nat Methods       Date:  2008-12       Impact factor: 28.547

9.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity.

Authors:  Robert C Edgar
Journal:  BMC Bioinformatics       Date:  2004-08-19       Impact factor: 3.169
  9 in total
  170 in total

1.  Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis.

Authors:  Maomeng Tong; Jonathan P Jacobs; Ian H McHardy; Jonathan Braun
Journal:  Curr Protoc Immunol       Date:  2014-11-03

2.  Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.

Authors:  Jiarong Guo; James R Cole; Qingpeng Zhang; C Titus Brown; James M Tiedje
Journal:  Appl Environ Microbiol       Date:  2015-10-16       Impact factor: 4.792

3.  Exoelectrogenic capacity of host microbiota predicts lymphocyte recruitment to the gut.

Authors:  Aaron Conrad Ericsson; Daniel John Davis; Craig Lawrence Franklin; Catherine Elizabeth Hagan
Journal:  Physiol Genomics       Date:  2015-04-07       Impact factor: 3.107

4.  Analysis of bacterial diversity in sponges collected from Chuuk and Kosrae Islands in Micronesia.

Authors:  In-Hye Jeong; Kyoung-Ho Kim; Hyi-Seung Lee; Jin-Sook Park
Journal:  J Microbiol       Date:  2014-01-04       Impact factor: 3.422

5.  Analysis of bacterial diversity in sponges collected off Chujado, an Island in Korea, using barcoded 454 pyrosequencing: analysis of a distinctive sponge group containing Chloroflexi.

Authors:  In-Hye Jeong; Kyoung-Ho Kim; Jin-Sook Park
Journal:  J Microbiol       Date:  2013-10-31       Impact factor: 3.422

6.  Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.

Authors:  Charles E Robertson; J Kirk Harris; Brandie D Wagner; David Granger; Kathy Browne; Beth Tatem; Leah M Feazel; Kristin Park; Norman R Pace; Daniel N Frank
Journal:  Bioinformatics       Date:  2013-09-10       Impact factor: 6.937

7.  Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients.

Authors:  Weimin Sun; Tangfu Xiao; Min Sun; Yiran Dong; Zengping Ning; Enzong Xiao; Song Tang; Jiwei Li
Journal:  Appl Environ Microbiol       Date:  2015-05-15       Impact factor: 4.792

8.  Bacterial community shift for monitoring the co-composting of oil palm empty fruit bunch and palm oil mill effluent anaerobic sludge.

Authors:  Mohd Huzairi Mohd Zainudin; Norhayati Ramli; Mohd Ali Hassan; Yoshihito Shirai; Kosuke Tashiro; Kenji Sakai; Yukihiro Tashiro
Journal:  J Ind Microbiol Biotechnol       Date:  2017-02-14       Impact factor: 3.346

9.  Gut Microbiota Analysis Results Are Highly Dependent on the 16S rRNA Gene Target Region, Whereas the Impact of DNA Extraction Is Minor.

Authors:  Anniina Rintala; Sami Pietilä; Eveliina Munukka; Erkki Eerola; Juha-Pekka Pursiheimo; Asta Laiho; Satu Pekkala; Pentti Huovinen
Journal:  J Biomol Tech       Date:  2017-02-28

10.  Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits.

Authors:  Juan E Pérez-Jaramillo; Víctor J Carrión; Mirte Bosse; Luiz F V Ferrão; Mattias de Hollander; Antonio A F Garcia; Camilo A Ramírez; Rodrigo Mendes; Jos M Raaijmakers
Journal:  ISME J       Date:  2017-06-06       Impact factor: 10.302
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.