Removing suffixes from GTDB taxonomy to improve qiime results

[SoilRotifer (Mike Robeson)]

@biojack

Then I remove suffixed from GTDB and repeated analysis. And at that one, Enteroccocus was found in GTDB as in Silva DB. The problem was in suffixes "Enterococcus", "Enterococcus_A", "Enterococcus_B", "Enterococcus_C", "Enterococcus_D", "Enterococcus_E", "Enterococcus_F", "Enterococcus_G", "Enterococcus_I", "Enterococcus_H". Classifier fail to distinguish them and there was underclassication for Enterococcus genus.

So if you providing (as I do) analysis within small region (like 16S V4) - removing GTDB suffixes could be way to go.

Thanks for sharing this!

We discuss this similar issue within the SILVA tutorial under the "Species-labels: caveat emptor!" section.

-Mike