Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

Eloe-Fadrosh, Emiley A.; Ivanova, Natalia N.; Woyke, Tanja; Kyrpides, Nikos C.

doi:10.1038/NMICROBIOL.2015.32

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

Journal Article · Sun Jan 31 23:00:00 EST 2016 · Nature Microbiology

DOI:https://doi.org/10.1038/NMICROBIOL.2015.32· OSTI ID:1379258

Eloe-Fadrosh, Emiley A. ^[1]; Ivanova, Natalia N. ^[1]; Woyke, Tanja ^[1]; Kyrpides, Nikos C. ^[1]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1379258

Journal Information:: Nature Microbiology, Journal Name: Nature Microbiology Journal Issue: 4 Vol. 1; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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