Literature DB >> 22161565

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.
© 2011 by John Wiley & Sons, Inc.

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Year:  2011        PMID： 22161565      PMCID： PMC3249058          DOI： 10.1002/0471250953.bi1007s36

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  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
  218 in total

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Authors:  Catherine A Fiala; Linda I Abbott; Cheryl D Carter; Stephen L Hillis; Jessica S Wolf; Meghan Schuster; Rachel Dulski; Elizabeth A Grice; Barbara A Rakel; Sue E Gardner
Journal:  J Adv Nurs       Date:  2018-05-07       Impact factor: 3.187

2.  Diversity of the vaginal microbiome correlates with preterm birth.

Authors:  Richard W Hyman; Marilyn Fukushima; Hui Jiang; Eula Fung; Larry Rand; Brittni Johnson; Kim Chi Vo; Aaron B Caughey; Joan F Hilton; Ronald W Davis; Linda C Giudice
Journal:  Reprod Sci       Date:  2013-05-28       Impact factor: 3.060

3.  Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome.

Authors:  Erin M Hill-Burns; Justine W Debelius; James T Morton; William T Wissemann; Matthew R Lewis; Zachary D Wallen; Shyamal D Peddada; Stewart A Factor; Eric Molho; Cyrus P Zabetian; Rob Knight; Haydeh Payami
Journal:  Mov Disord       Date:  2017-02-14       Impact factor: 10.338

4.  The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants.

Authors:  Masaru Tanaka; Masafumi Sanefuji; Seiichi Morokuma; Misako Yoden; Rie Momoda; Kenji Sonomoto; Masanobu Ogawa; Kiyoko Kato; Jiro Nakayama
Journal:  Gut Microbes       Date:  2019-09-24

5.  A mole rat's gut microbiota suggests selective influence of diet on microbial niche space and evolution.

Authors:  Linda Ren; Robert A Holzknecht; Zoie E Holzknecht; Sanet H Kotzé; Dawn E Bowles; Shu S Lin; Erin A McKenney; William Parker
Journal:  Exp Biol Med (Maywood)       Date:  2019-02-13

6.  Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing.

Authors:  Chao Qi; Peter Hountras; Chiagozie Ononye Pickens; James M Walter; Jacqueline M Kruser; Benjamin D Singer; Patrick Seed; Stefan J Green; Richard G Wunderink
Journal:  J Med Microbiol       Date:  2019-05-28       Impact factor: 2.472

7.  The Impact of Human Immunodeficiency Virus Infection on Gut Microbiota α-Diversity: An Individual-level Meta-analysis.

Authors:  Susan A Tuddenham; Wei Li A Koay; Ni Zhao; James R White; Khalil G Ghanem; Cynthia L Sears
Journal:  Clin Infect Dis       Date:  2020-02-03       Impact factor: 9.079

Review 8.  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

9.  Fructose stimulated de novo lipogenesis is promoted by inflammation.

Authors:  Jelena Todoric; Giuseppe Di Caro; Saskia Reibe; Darren C Henstridge; Courtney R Green; Alison Vrbanac; Fatih Ceteci; Claire Conche; Reginald McNulty; Shabnam Shalapour; Koji Taniguchi; Peter J Meikle; Jeramie D Watrous; Rafael Moranchel; Mahan Najhawan; Mohit Jain; Xiao Liu; Tatiana Kisseleva; Maria T Diaz-Meco; Jorge Moscat; Rob Knight; Florian R Greten; Lester F Lau; Christian M Metallo; Mark A Febbraio; Michael Karin
Journal:  Nat Metab       Date:  2020-08-24

10.  Intestinal dysbiosis and bacterial enteroinvasion in a murine model of Hirschsprung's disease.

Authors:  Joseph F Pierre; Amanda J Barlow-Anacker; Christopher S Erickson; Aaron F Heneghan; Glen E Leverson; Scot E Dowd; Miles L Epstein; Kenneth A Kudsk; Ankush Gosain
Journal:  J Pediatr Surg       Date:  2014-08       Impact factor: 2.545
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