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Metagenomic species profiling using universal phylogenetic marker genes
Shinichi Sunagawa1, Daniel R Mende, Georg Zeller
1European Molecular Biology Laboratory, Heidelberg, Germany.
Nature Methods
|October 22, 2013
Summary
A new method using metagenomic operational taxonomic units (mOTUs) quantifies microorganisms from shotgun sequencing. This approach captures significantly more species abundance and richness than current reference genome-based methods.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Metagenomic studies aim to characterize microbial communities.
- Current methods often rely on reference genomes, potentially missing uncharacterized species.
Purpose of the Study:
- To develop a novel method for quantifying known and unknown microorganisms at species-level resolution.
- To assess the limitations of existing reference genome-based approaches in metagenomics.
Main Methods:
- Development of a method to establish metagenomic operational taxonomic units (mOTUs).
- Utilized single-copy phylogenetic marker genes for mOTU delineation.
- Applied the mOTU method to shotgun sequencing data from 252 human fecal samples.
Main Results:
- The mOTU method successfully quantified microorganisms at species-level resolution.
- On average, 43% of species abundance and 58% of species richness were not captured by current reference genome-based methods.
- Identified a substantial portion of microbial diversity missed by existing techniques.
Conclusions:
- The developed mOTU method provides a more comprehensive assessment of microbial community composition.
- Reference genome-based methods significantly underestimate microbial diversity in metagenomic datasets.
- This advancement offers improved tools for microbiome research and microbial discovery.
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