Dear everybody,

I am planning a new microbial metagenomic study. There are several new kits available (such as “QIAgen 16S/ITS Region Panel” and “Swift Amplicon 16S+ITS Panel” kits) that allows to create amplicon libraries of different regions for the same sample. The goal (and promise from manufacturer) is to improve taxonomic assignment, with better lower alpha diversity assignment that should come from greater sequencing coverage of the 16S gene.

For example, I could create libraries with both V1V2 region and V3V4 region (together they cover half the 16S gene). However, the reads from these two regions do not overlap (I checked the primers). Therefore, I wonder the following: is it possible and how to "combine" the information from two non-overlapping regions to perform taxonomic/OTUs assignment?

I know how to perform taxonomic assignment when you have one region per sample. Since the two regions in the example do not overlap, I cannot assemble the two regions into one contig (one would have to use V1V2 and V2V3 region, for example). One could separate samples reads according to region, and analyse them individually, but I believe this would somewhat defeat the purpose of the sequencing multiple regions.

Perhaps there are ways yet unknown to me. I would be very glad if someone could explain to me, refer to papers that use such methodology or kits.

I thank you in advance for any help

M.