Coverage evaluation of universal bacterial primers using the metagenomic datasets.

ABSTRACT:

Background

The coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RDP) to assess the coverage of 8 widely used bacterial primers.

Results

The coverage rates for bacterial primers were found to be overestimated by previous studies that only investigated the RDP because of PCR amplification bias in the sequence composition of the dataset. In the RDP, the non-co

SUBMITTER: Mao DP 

PROVIDER: S-EPMC3445835 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature