One of my studies (A) involve sequencing the microbiome. After selecting the variable region and the primers for the targeted region of the 16S sequence. The samples were sent to a platform.
For another study (B) we used the same strategy (same primers, region, machine...) but another platform. However we obtained from this platform a lot more sequences:
In study A the mean sequences per sample are 10k, while in the study B the mean sequences per sample are 80k
I consulted with others and it seems that the study A we under-sampled and in study B we over-sampled.
I can understand that by under-sampling we didn't obtain enough reads to be sure about the microbiome present in the sample. But what does it mean to over-sampling?
That expert I consulted suggested normalize the data to fewer sequences, discarding information we already have. I can understand that the sequencing has errors and can create chimeras but the resulting consensus sequences of the OTUs have found a match with databases of microorganisms. What or how should I take into account that I over-sampled?