type strains of 16S rRNA gene sequences for most bacteria and archaea are available on public databases such as NCBI, but not validated. Therefore, the secondary databases that collect only 16S rRNA sequences are widely use, such as EzTaxon-e, Ribosomal Databases Project (RDP), SILVA, Greengene.

So what are you looking into, prokaryotes or eukaryote? As for my case, I will choose greengene as database to analysis prokaryotes. It address the limitations of public repositories by providing chimera screening, standard alignment and taxonomic classification using multiple published taxonomies, including RDP etc. 

SILVA is more likelying working for eukaryotes.

Actually, I just start to look into these databases these days. Hopefully we can communicate more and learn more

hi ..

thanks a lot for your informative reply..

i am working with environmental samples.. estuary, sea , reef ecosystem, sponges..

i study their microbial diversity based on clone library method. EZTaxon is for cultivable isolates, right?

It was, but since 2012, ExTaxon was extended to include uncultured prokaryotes and changed the name of the database to ExTaxon-e

Sorry, didn't actually answer your questions on the differences of SILVA based taxonomy or RDP classifier