Someone recently asked me whether it would be interesting to use Unique Molecular Identifiers (UMIs - used in RNA-seq) for 16S rRNA sequencing in order to have a closer estimate of the number of each 16S in a given sample. The idea is that putting a unique sequence tag on each 16S molecule before PCR allows the identification of PCR duplicates and consequently leads to a better estimate of the true taxa abundances.
I know that that has been rarely (if ever) used in the literature, so I assume it is not a great idea, but I still can’t say the reason. Why are we not using UMIs for microbiome amplicon-sequencing?
My first guess is that by including UMIs the region of interest will be shortened, decreasing taxonomic resolution. Any additional points am I missing?