Hello,
looking over the documentation, I did not find any approach to this problem. The gene copy number, however, should influence the relative abundance estimations and information from databases like rRNDB could be used to improve these estimates. Is it common to ignore the copy number issue with 16S data? Is there any way to use such information in mothur?
Yeah, this is the little dark secret of microbial ecology. One could certainly try to correct for multiple copies (we’ll leave this to someone else), but it would be very hard. The data in the rRNDB is for cultured bugs, and most of what’s out there is uncultured. Considering the wide spread within some groups, it quickly becomes a headache. What helps us to sleep at night is the thought that we’re looking for are relative changes and so even if we don’t get the exact relationship between the abundance of OTU1 and OTU2, when their population sizes shift, we should be able to detect that regardless of the copy number. Shhh… don’t tell anyone. 
Pat
Thanks for this information. I guess this means that one should simply not put to much focus on relative intra-sample abundances but more on the community structure and inter-sample ratios. I thought about doing a phylogenetic nearest-neighbor copy number correction as some publications suggest rRNA copy number consistency across clades. Unfortunately rrndb seems to be an online ressource only. No downloads to give it a try…
Johannes