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Title: Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

Abstract

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 in this paper, 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. In conclusion, these results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.

Authors:
 [1];  [1];  [1];  [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379258
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Microbiology
Additional Journal Information:
Journal Volume: 1; Journal Issue: 4; Journal ID: ISSN 2058-5276
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Environmental microbiology; Metagenomics; Microbial ecology; Microbiome

Citation Formats

Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., Woyke, Tanja, and Kyrpides, Nikos C. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. United States: N. p., 2016. Web. doi:10.1038/NMICROBIOL.2015.32.
Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., Woyke, Tanja, & Kyrpides, Nikos C. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. United States. doi:10.1038/NMICROBIOL.2015.32.
Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., Woyke, Tanja, and Kyrpides, Nikos C. Mon . "Metagenomics uncovers gaps in amplicon-based detection of microbial diversity". United States. doi:10.1038/NMICROBIOL.2015.32. https://www.osti.gov/servlets/purl/1379258.
@article{osti_1379258,
title = {Metagenomics uncovers gaps in amplicon-based detection of microbial diversity},
author = {Eloe-Fadrosh, Emiley A. and Ivanova, Natalia N. and Woyke, Tanja and Kyrpides, Nikos C.},
abstractNote = {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 in this paper, 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. In conclusion, these results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.},
doi = {10.1038/NMICROBIOL.2015.32},
journal = {Nature Microbiology},
number = 4,
volume = 1,
place = {United States},
year = {Mon Feb 01 00:00:00 EST 2016},
month = {Mon Feb 01 00:00:00 EST 2016}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 30 works
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Works referenced in this record:

WebLogo: A Sequence Logo Generator
journal, May 2004

  • Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
  • Genome Research, Vol. 14, Issue 6, p. 1188-1190
  • DOI: 10.1101/gr.849004