Best 16S Region ?

Question

[Dph]

Does someone have an idea of the best 16S gene region to amplify with NGS in order to assess microbial (bacterial) diversity in environmental samples ? cheers

[Istvan Albert]

What do you mean best? Do you refere to selecting from among the universal primers? http://en.wikipedia.org/wiki/16S_ribosomal_RNA#Universal_Primers

Answer 1

[Zhidkov]

You can use information from The Ribosomal Database Project (RDP):[?] http://rdp.cme.msu.edu/ [?] or Silva database[?] http://www.arb-silva.de/ [?]

Ilia

Answer 2

[Larry_Parnell]

Our colleagues use one 16S amplicon across the V3-V5 region.

[Dph]

and some other use the V6 one...