%0 Journal Article
%T Coverage evaluation of universal bacterial primers using the metagenomic datasets
%A Dan-Ping Mao
%A Quan Zhou
%A Chong-Yu Chen
%A Zhe-Xue Quan
%J BMC Microbiology
%D 2012
%I BioMed Central
%R 10.1186/1471-2180-12-66
%X 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-coverage rates for all primers except 27F were £¿6%, while in the metagenomic datasets, most were £¿10%. If one considers that a single mismatch near the 3¡ä end of the primer might greatly reduce PCR efficiency, then some phylum non-coverage rates would change by more than 20%. Primer binding-site sequence variants that could not pair with their corresponding primers are discussed.Our study revealed the potential bias introduced by the use of universal bacterial primers in the assessment of microbial communities. With the development of high-throughput, next-generation sequencing techniques, it will become feasible to sequence more of the hypervariable regions of the bacterial 16S rRNA gene. This, in turn, will lead to the more frequent use of the primers discussed here.
%U http://www.biomedcentral.com/1471-2180/12/66/abstract