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Updated: Jun 19, 2026
11:22
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing
Patrick D Schloss1, Sarah L Westcott, Thomas Ryabin
1Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA. pschloss@umich.edu
Applied and Environmental Microbiology
|October 6, 2009
Summary
Mothur is a versatile software package for analyzing microbial community sequence data. It efficiently processes large datasets, enabling comprehensive analysis of microbial diversity from raw sequences to diversity metrics.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- Analyzing microbial community sequence data is crucial for understanding ecological roles.
- Previous tools often require multiple software packages, complicating the analysis workflow.
- A comprehensive, integrated software solution is needed for efficient sequence data analysis.
Purpose of the Study:
- To introduce mothur, a comprehensive software package for analyzing microbial community sequence data.
- To demonstrate the utility of mothur using a case study involving marine microbial communities.
- To highlight the efficiency and power of mothur for high-throughput sequencing data analysis.
Main Methods:
- Utilized mothur for sequence trimming, screening, and alignment.
- Applied mothur for distance calculations and operational taxonomic unit (OTU) assignment.
- Employed mothur to describe alpha and beta diversity metrics for marine samples.
Main Results:
- Successfully analyzed over 222,000 16S rRNA gene sequences from marine samples.
- Mothur performed sequence processing, taxonomic assignment, and diversity analysis.
- The entire analysis, including diversity metrics, was completed in under 2 hours on a laptop.
Conclusions:
- Mothur provides a flexible and powerful platform for comprehensive microbial community analysis.
- The software package streamlines complex workflows, from raw sequence data to diversity assessment.
- Mothur offers an efficient solution for analyzing large-scale sequencing datasets, even on standard hardware.
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