Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Applied and Environmental Microbiology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Methods

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

Patrick D. Schloss, 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
Patrick D. Schloss
1Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
2Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: pschloss@umich.edu
Sarah L. Westcott
1Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
2Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Thomas Ryabin
1Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Justine R. Hall
3Department of Biology, University of New Mexico, Albuquerque, New Mexico
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Martin Hartmann
4Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Emily B. Hollister
5Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ryan A. Lesniewski
6Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brian B. Oakley
7Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Donovan H. Parks
8Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Courtney J. Robinson
2Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jason W. Sahl
9Environmental Science and Engineering, Colorado School of Mines, Golden, Colorado
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Blaz Stres
10Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gerhard G. Thallinger
11Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David J. Van Horn
2Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Carolyn F. Weber
12Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/AEM.01541-09
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • FIG. 1.
    • Open in new tab
    • Download powerpoint
    FIG. 1.

    Description and comparison of the eight samples analyzed by Sogin et al. (27). The dendrogram to the left represents the similarity of the samples based on the membership-based Jaccard coefficient calculated using Chao1 estimated richness values. The dendrogram on the right represents the similarity of the samples based on the structure-based θYC coefficient. The distance from the tip of the dendrogram to the root is 0.50 for both trees.

  • FIG. 2.
    • Open in new tab
    • Download powerpoint
    FIG. 2.

    Rarefaction curves describing the dependence of discovering novel OTUs as a function of sampling effort for OTUs defined at a 0.10 distance cutoff. The curves for FS312 and FS396 climb to 3,095 and 2,804 OTUs after sampling of 54,894 and 80,769 sequences, respectively.

Tables

  • Figures
  • TABLE 1.

    Features from preexisting software that have been integrated into mothura

    Existing toolDescriptionImplementation in mothurReference(s)
    Pyrosequencing pipeline (RDP)Online tool that trims and deconvolutes sequences using user-supplied dataStand-alone implementation; increased speed; greater flexibility; additional screening options 3
    NAST, SINA, and RDP alignersOnline tools that align user-supplied sequences with specific databasesStand-alone implementation; can utilize multiple processors; increased speed; greater flexibility; open source 3-5, 20
    DNADISTCalculates pairwise distances between sequences (does not penalize for gaps)Can utilize multiple processors; more efficient use of RAM; various ways to penalize gaps 6
    DOTUR and CD-HITAssigns sequences to OTUs, constructs sampling curves, and estimates richness and diversityMore efficient clustering; requires less memory; additional calculators; greater flexibility 10, 22
    SONSCalculates estimates of the fraction and richness of OTUs shared between communitiesGenerates dendrograms, heat maps, and Venn diagrams; additional calculators; greater flexibility 23
    ∫-LIBSHUFFUses the Cramer-von Mises statistic to test whether two communities have the same structureEliminates the need for a sorted distance matrix; can specify pairwise comparisons 25, 26
    TreeClimberUses a parsimony-based test to determine whether two or more communities have the same structureGreater flexibility; can specify pairwise comparisons 14, 15, 24
    UniFracCompares the phylogenetic distance between communities to detect differences in community structureStand-alone implementation; greater flexibility; can input bootstrap trees 12
    • ↵ a In all cases, modifications have been made to the mothur implementation of the algorithms for greater flexibility, speed, and resource utilization.

  • TABLE 2.

    Measures of α diversity for the samples characterized by Sogin et al. (27) for three OTU definitionsa

    SampleNo. of reads0.030.050.10
    OTUChaoH′OTUChaoH′OTUChaoH′
    53R12,7251,5993,2225.291,4202,6225.191,0531,7334.81
    55R9,8481,4692,9945.541,3022,4965.439621,7415.03
    112R15,0572,2585,1895.912,0324,2825.791,5842,9925.44
    115R16,1811,7493,6005.311,5523,0885.211,1351,9194.83
    13713,8311,4252,6875.441,2952,4305.369891,6455.07
    13812,9381,4252,5425.241,2532,1315.149571,4794.81
    FS31254,8944,37110,6915.233,9489,2595.163,0956,4094.94
    FS39680,7694,35910,2084.673,8068,6094.602,8045,4374.42
    • ↵ a 0.03, 0.05, and 0.10 are the OTU cutoffs in distance units. OTU signifies the number of OTUs observed, Chao signifies the Chao1 estimated minimum number of OTUs, and H′ signifies the nonparametric Shannon diversity index.

PreviousNext
Back to top
Download PDF
Citation Tools
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss, 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
Applied and Environmental Microbiology Nov 2009, 75 (23) 7537-7541; DOI: 10.1128/AEM.01541-09

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Applied and Environmental Microbiology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
(Your Name) has forwarded a page to you from Applied and Environmental Microbiology
(Your Name) thought you would be interested in this article in Applied and Environmental Microbiology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss, 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
Applied and Environmental Microbiology Nov 2009, 75 (23) 7537-7541; DOI: 10.1128/AEM.01541-09
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • Introducing mothur.
    • Object oriented, responsive, free, and platform independent.
    • Open documentation and support.
    • Example workflow: the ocean's rare biosphere.
    • Looking forward.
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

biodiversity
Computational Biology
metagenomics
Software

Related Articles

Cited By...

About

  • About AEM
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #AppEnvMicro

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

 

Print ISSN: 0099-2240; Online ISSN: 1098-5336