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Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
Patrick D Schloss1, Jo Handelsman
1Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Dr., Madison, WI 53706, USA.
Applied and Environmental Microbiology
|March 5, 2005
Summary
Researchers developed DOTUR, a program for statistically analyzing microbial community composition using genetic distances. This method accurately assigns sequences to operational taxonomic units (OTUs) and reveals that soil microbial communities require extensive sequencing for reliable diversity estimates.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- Qualitative data on microbial communities is abundant, but quantitative statistical methods for comparing lineage composition are lacking.
- Accurate quantification and comparison of microbial lineages are crucial for understanding biodiversity and ecological roles.
Purpose of the Study:
- To present a novel statistical method and software (DOTUR) for assigning genetic sequences to operational taxonomic units (OTUs).
- To enable robust quantification and comparison of microbial community composition based on genetic distances.
Main Methods:
- Development of the DOTUR program, utilizing furthest, average, or nearest neighbor algorithms for OTU assignment based on genetic distance thresholds.
- Construction of rarefaction and collector's curves using OTU frequencies to assess richness and diversity.
- Analysis of 16S rRNA gene libraries from diverse environments (Scottish soil, Amazonian soil, Sargasso Sea).
Main Results:
- DOTUR rapidly and reliably assigned sequences to OTUs, identifying prior inconsistencies in OTU assignment.
- Soil microbial communities from Scotland and the Amazon lacked sufficient sequence data for statistically confident comparisons of lineage numbers or robust species richness estimates at a 3% genetic distance threshold.
- Sargasso Sea microbial community richness began to plateau after sequencing 690 samples at the 3% distance level, suggesting soil communities require significantly more sequences (>10,000) for similar saturation.
Conclusions:
- The DOTUR program provides a reliable statistical framework for microbial community analysis.
- Current sequencing efforts for soil microbial communities are often insufficient for accurate diversity assessment and comparison.
- Substantially larger sequencing depths are necessary to adequately characterize the diversity of soil microbial communities.