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Literature DB >> 19801464

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

Patrick D Schloss¹, Sarah L Westcott, Thomas Ryabin, Justine R Hall, Martin Hartmann, Emily B Hollister, Ryan A Lesniewski, Brian B Oakley, Donovan H Parks, Courtney J Robinson, Jason W Sahl, Blaz Stres, Gerhard G Thallinger, David J Van Horn, Carolyn F Weber.

Abstract

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Mesh：

Year: 2009 PMID： 19801464 PMCID： PMC2786419 DOI： 10.1128/AEM.01541-09

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

23 in total

1. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures.

Authors: A E McCaig; L A Glover; J I Prosser
Journal: Appl Environ Microbiol Date: 1999-04 Impact factor: 4.792

Review 2. Phylogenetic approaches for describing and comparing the diversity of microbial communities.

Authors: Andrew P Martin
Journal: Appl Environ Microbiol Date: 2002-08 Impact factor: 4.792

3. Integration of microbial ecology and statistics: a test to compare gene libraries.

Authors: Patrick D Schloss; Bret R Larget; Jo Handelsman
Journal: Appl Environ Microbiol Date: 2004-09 Impact factor: 4.792

4. ARB: a software environment for sequence data.

Authors: Wolfgang Ludwig; Oliver Strunk; Ralf Westram; Lothar Richter; Harald Meier; Arno Buchner; Tina Lai; Susanne Steppi; Gangolf Jobb; Wolfram Förster; Igor Brettske; Stefan Gerber; Anton W Ginhart; Oliver Gross; Silke Grumann; Stefan Hermann; Ralf Jost; Andreas König; Thomas Liss; Ralph Lüssmann; Michael May; Björn Nonhoff; Boris Reichel; Robert Strehlow; Alexandros Stamatakis; Norbert Stuckmann; Alexander Vilbig; Michael Lenke; Thomas Ludwig; Arndt Bode; Karl-Heinz Schleifer
Journal: Nucleic Acids Res Date: 2004-02-25 Impact factor: 16.971

5. 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

6. Introducing TreeClimber, a test to compare microbial community structures.

Authors: Patrick D Schloss; Jo Handelsman
Journal: Appl Environ Microbiol Date: 2006-04 Impact factor: 4.792

7. Evaluating different approaches that test whether microbial communities have the same structure.

Authors: Patrick D Schloss
Journal: ISME J Date: 2008-01-31 Impact factor: 10.302

8. Culture-independent identification of microorganisms that respond to specified stimuli.

Authors: J Borneman
Journal: Appl Environ Microbiol Date: 1999-08 Impact factor: 4.792

9. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples.

Authors: D R Singleton; M A Furlong; S L Rathbun; W B Whitman
Journal: Appl Environ Microbiol Date: 2001-09 Impact factor: 4.792

10. 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

2000 in total

1. Interleukin-22 regulates the complement system to promote resistance against pathobionts after pathogen-induced intestinal damage.

Authors: Mizuho Hasegawa; Shoko Yada; Meng Zhen Liu; Nobuhiko Kamada; Raúl Muñoz-Planillo; Nhu Do; Gabriel Núñez; Naohiro Inohara
Journal: Immunity Date: 2014-10-16 Impact factor: 31.745

2. Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach.

Authors: Juliana Young; Joseph H Skarlupka; Madison S Cox; Rafael Tassinari Resende; Amelie Fischer; Kenneth F Kalscheur; Jennifer C McClure; John B Cole; Garret Suen; Derek M Bickhart
Journal: Appl Environ Microbiol Date: 2020-08-18 Impact factor: 4.792

3. The role of Gr-1(+) cells and tumour necrosis factor-α signalling during Clostridium difficile colitis in mice.

Authors: Andrew J McDermott; Kathryn E Higdon; Ryan Muraglia; John R Erb-Downward; Nicole R Falkowski; Roderick A McDonald; Vincent B Young; Gary B Huffnagle
Journal: Immunology Date: 2015-04 Impact factor: 7.397

4. Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period.

Authors: Joshua R Stokell; Raad Z Gharaibeh; Timothy J Hamp; Malcolm J Zapata; Anthony A Fodor; Todd R Steck
Journal: J Clin Microbiol Date: 2014-11-12 Impact factor: 5.948

5. 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

Review 6. Potential for Monitoring Gut Microbiota for Diagnosing Infections and Graft-versus-Host Disease in Cancer and Stem Cell Transplant Patients.

Authors: Andrew Y Koh
Journal: Clin Chem Date: 2017-07-18 Impact factor: 8.327

10. 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