16S library prep + Nebnext

[floresu]

I want to characterize some microbial communities by Miseq sequencing of 16S libraries using the primers 341F/805R (reported in Klindworth 2012). Illumina's "16S Metagenomic Sequencing Library Preparation" uses the same primers but modified to include overhang sequences. Currently in the lab we have the NebNext DNA Library Prep Kit.

What would be the difference of preparing the libraries (using NebNext) with PCR products with and without overhang seqs?

Does it affect overall analysis sensitivity?

I would appreciate any advice you guys could give me.

Thanks in advance!

[luc]

The Illumina protocol will more convenient in the long run. If one can avoid ligations and the other library prep steps, I would suggest to do so.