Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

@article{EloeFadrosh2016MetagenomicsUG,
  title={Metagenomics uncovers gaps in amplicon-based detection of microbial diversity},
  author={Emiley A. Eloe-Fadrosh and Natalia N. Ivanova and Tanja Woyke and Nikos C. Kyrpides},
  journal={Nature Microbiology},
  year={2016},
  volume={1}
}
Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences… 
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