Can I use the xGen™ Amplicon 16S and ITS1 Panels together?
The xGen™ 16S Amplicon Panel v2 and xGen ITS1 Amplicon Panel can be used together to target both bacteria/archaea and fungi.
There is no intrinsic problem in the panels’ chemistry that prevents this. However, if preserving and quantifying relative abundances between these two target lineages are NOT part of the study, we recommend that 16S and ITS1 libraries are made separately before pooling for sequencing.
This is to minimize the potential problem that 16S amplicons could become dominant over that of ITS1 if two primer pools were combined for multiplex PCR in the workflow, resulting in unbalanced sequence depth for the two target regions.
This problem is due to the presence of multiple 16S regions in the genome and bacteria/archaea being more prevalent in most samples.