Some studies point out that 16S and WGS-derived bacterial community compositions are significantly different.
But I have not seen any works actually comparing the accuracy of these 2 methods. What if we apply both of them to a gnotobiotic community? Which one will be more accurate?
While 16S produce more OTUs (possibly due to PCR chimeras), WGS might omit rare bacteria.
Both these methods produce protocol-dependent result, so even in a gnotobiotic experiment the true accuracy might be compromised by implementing a bad protocol for a possibly better method.
But what type of data should I use given the choice (e.g as in HMP that provides both 16S and WGS data)?