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Metagenomics uncovers gaps in amplicon-based detection of microbial diversity


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 might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. These results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.

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Figure 1: Primer fidelity for commonly used environmental PCR primers.
Figure 2: Habitat distribution of taxonomic novelty.


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This work was conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility (contract no. DE-AC02-05CH11231), and used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US Department of Energy (contract no. DE-AC02-05CH11231).

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E.A.E.-F., N.N.I., T.W. and N.C.K. designed the project, analysed the data and wrote the manuscript. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Nikos C. Kyrpides.

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The authors declare no competing financial interests.

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Supplementary Information

Supplementary Figures 1–3, Supplementary Tables 1,2. (PDF 273 kb)

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Eloe-Fadrosh, E., Ivanova, N., Woyke, T. et al. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nat Microbiol 1, 15032 (2016).

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