Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
Eloe-Fadrosh EA, Ivanova NN, Woyke T, Kyrpides NC
Nat Microbiol. 2016. doi: 10.1038/nmicrobiol.2015.32
COMMENT: In this publication the authors compared SSU rRNA gene sequences (³ 1000 bp) with commonly used PCR primer sets and generated a weighted score based on the number of mismatches. The results showed that at least 10% of environmental bacterial (mostly members of the recently described Candidate Phyla Radiation) and/or archaeal sequences based on metagenomics data might be missed using a targeted PCR survey.
In addition, the authors analyse the habitat distribution of those unclassified sequences in order to provide insight into the suite of environmental locales potentially hosting as yet uncharacterized microbial life.