It's been common to use primer for variable regions in 16s DNA but I heard that it's not highly trusted anymore. I wonder what primer is now used for DGGE and where I can get it.
You can use a nested PCR approach. In the first PCR, the universal bacterial primers 27F (5´-AGA GTT TGA TCC TGG CTC AG-3´) and 1494R (5´-TAC GGT TAC CTT GTT ACG AC-3´) can be used to amplify ca. 1450 bp of the 16S rRNA gene . For DGGE analysis, you can amplify the 410-bp rRNA gene fragment with primers F968-GC-clamp (5′-GC-clamp-AACGCGAAGAACCTTAC-3′) and R1401 (5′-GCGTGTGTACAAGACCC-3′) (Integrated DNA Technologies, BVBA, Munich, Germany) (Nubel et al., 1996) using as template 1 μL of the product obtained from the first PCR.
While metagenomics would of course give you much more and better information about your communities, it still has the same problem as DGGE in terms of PCR bias. So, the choice of primer will influence your results independent if you use DGGE or metagenomic sequencing.
Depending of what you want to get out of your analysis, my suggestion would be to do the analysis with two or more different 16S primers to reduce the influence of PCR bias and see if they lead to similar results. A good resource for 16S primers that can be used for various applications and their coverage can be found in the paper
Nucleic Acids Res. 2013 Jan 7;41(1):e1. doi: 10.1093/nar/gks808. Epub 2012 Aug 28.
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO.
Good luck with your analysis.