V4 region - Archaea and Bacteria at genus level

Hi, I ran the SOP on targeted V4 region of the 16S rRNA sequences. I used the latest mothur version, Silva Database v132, and RDP classifier version 18. I aligned the Silva Database to the V4 region without the primers. After performing the Phylotype based analysis and opening the shared and taxonomy files, many samples show quantity 0 in archaea and bacteria, which I didn’t expect.
So I am wondering if I misaligned the database, or if it’s a result of bad classification.
For some reason mothur didn’t save a logfile on mac, but I have the results saved for reference.

I am looking for the genus level.
At the remove.lineage command, I only removed the unknowns and kept all others (Archaea were classified, but few of the samples shows a very low abundance while all others are at 0. Something similar is observed with Bacteria).

I highly appreciate the help!

Can you post the shared file here? If a sample doesn’t doesn’t have any bacteria or archaea then it shouldn’t show up in the shared file. So, I’m a bit confused by what you’re describing.


I am not able to post the file here. Can I share it by mail?

sure - pschloss / umich.edu