article Open AccessTop 1% cited
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Applied and Environmental Microbiology · 2009 · Vol. 75(23) · pp. 7537–7541
Patrick D. Schloss✉(University of Michigan)Sarah L. Westcott(University of Michigan)Thomas Ryabin(University of Massachusetts Amherst)Justine R. Hall(University of New Mexico)Martin Hartmann(University of British Columbia)Emily B. Hollister(Texas A&M University)Ryan A. Lesniewski(University of Minnesota)Brian B. Oakley(University of Warwick)Donovan H. Parks(Dalhousie University)Courtney J. Robinson(University of Michigan)Jason W. Sahl(Colorado School of Mines)Blaž Stres(University of Ljubljana)Gerhard Thallinger(Graz University of Technology)David J. Horn(University of Michigan)Carolyn F. Weber(Louisiana State University)
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.
Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesGut microbiota and healthLaptopSoftwarePyrosequencingComputer scienceMetagenomicsData miningComputational biologyBiologySoftware engineeringGenetics
MeSH terms
Environmental MicrobiologySoftwareSequence Analysis, DNAComputational BiologyBiodiversityMetagenomics
Funding
- National Science Foundation
- Alfred P. Sloan Foundation
Citations
21,514
FWCI
370.64
field-weighted impact
References
30
Percentile
100%
vs. same field & year
Citations per year
Cited by
Distinct soil microbial diversity under long-term organic and conventional farming
The ISME Journal · 2014 · 1,403 citations
Phylogenetic conservatism of functional traits in microorganisms
The ISME Journal · 2012 · 596 citations
Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management
Phytopathology · 2016 · 364 citations
Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil
Soil Biology and Biochemistry · 2016 · 1,029 citations
The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation
The ISME Journal · 2013 · 1,069 citations
Vertical mother–neonate transfer of maternal gut bacteria via breastfeeding
Environmental Microbiology · 2013 · 596 citations
Gut microbiota are related to Parkinson's disease and clinical phenotype
Movement Disorders · 2014 · 1,948 citations
Microbiota transplantation restores normal fecal bile acid composition in recurrent<i>Clostridium difficile</i>infection
American Journal of Physiology-Gastrointestinal and Liver Physiology · 2013 · 423 citations
References
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
Applied and Environmental Microbiology · 2006 · 11,173 citations
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Nucleic Acids Research · 2007 · 6,832 citations
Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation
Infection and Immunity · 2009 · 560 citations
ARB: a software environment for sequence data
Nucleic Acids Research · 2004 · 6,783 citations
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Bioinformatics · 2006 · 11,865 citations
Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness
Applied and Environmental Microbiology · 2005 · 2,505 citations
UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context
BMC Bioinformatics · 2006 · 1,461 citations
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Applied and Environmental Microbiology · 2005 · 8,476 citations
Citation Network
How this paper connects to the literature. Drag to explore, click any node to open that paper.