For bacterial profiling please choose at least on 16S target, for fungal profiling at least one ITS target. For taxonomic profiling or archea please selcet our archeal 16S target.
As each primer set fails to amplify certain species we recommend that you carefully check the literature available about the limitations of each primer set. It is recommended to use multiple primer combinations to capture the entire community (e.g. Ihrmark et al., 2012; Toju et al., 2012).