Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper posted (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).

Taxonomy in OTU tables

There are no practically useful standards for including taxonomy in OTU tables. Each program has its own standards for formatting, and it is not practice for USEARCH to support all the file formats out there. You will therefore need to write your own script to re-format taxonomy strings and embed them into your OTU table.