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Applied and Environmental Microbiology, December 2009, p. 7537-7541, Vol. 75, No. 23
0099-2240/09/$08.00+0     doi:10.1128/AEM.01541-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities{triangledown}

Patrick D. Schloss,1,2* Sarah L. Westcott,1,2 Thomas Ryabin,1 Justine R. Hall,3 Martin Hartmann,4 Emily B. Hollister,5 Ryan A. Lesniewski,6 Brian B. Oakley,7 Donovan H. Parks,8 Courtney J. Robinson,2 Jason W. Sahl,9 Blaz Stres,10 Gerhard G. Thallinger,11 David J. Van Horn,2 and Carolyn F. Weber12

Department of Microbiology, University of Massachusetts, Amherst, Massachusetts,1 Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan,2 Department of Biology, University of New Mexico, Albuquerque, New Mexico,3 Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada,4 Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas,5 Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota,6 Department of Biological Sciences, University of Warwick, Coventry, United Kingdom,7 Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada,8 Environmental Science and Engineering, Colorado School of Mines, Golden, Colorado,9 Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia,10 Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria,11 Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana,12

Received 30 June 2009/ Accepted 26 September 2009

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 β 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.

* Corresponding author. Mailing address: Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109. Phone: (734) 647-5801. Fax: (734) 764-3562. E-mail: pschloss{at}umich.edu

{triangledown} Published ahead of print on 2 October 2009.

Applied and Environmental Microbiology, December 2009, p. 7537-7541, Vol. 75, No. 23
0099-2240/09/$08.00+0     doi:10.1128/AEM.01541-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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