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, 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.
authors: Joint Genome Institute, Walnut Creek, California 94598, USA.
authors: Emiley A
authors: EA
authors: Eloe-Fadrosh
authors: Joint Genome Institute, Walnut Creek, California 94598, USA.
authors: Natalia N
authors: NN
authors: Ivanova
authors: Joint Genome Institute, Walnut Creek, California 94598, USA.
authors: Tanja
authors: T
authors: Woyke
authors: Joint Genome Institute, Walnut Creek, California 94598, USA.
authors: Nikos C
authors: NC
authors: Kyrpides
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics*; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D044822:Biodiversity; D016000:Cluster Analysis; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D004783:Environmental Microbiology; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S