I have made major changes to the taxonomic table of the database, which is now compatible with SILVA taxonomy. Although SILVA taxonomy does not match the taxonomy in the List of Prokaryotic names with Standing in Nomenclature the change was necessary because new studies in FoodMicrobionet are processed using SILVA v138 and this was causing inconsistencies in the higher level taxonomy of taxa (i.e. the same genus might potentially have a different lineage depending on when it was added to the database) and this, in turn, would prevent correct aggregation at levels higher than genus. In case you want to know, I did compare taxonomic assignments done with SILVA v132 and v138 for five studies using different 16S RNA gene regions as a target. The same sequence was assigned to a different “taxon” in as many as 70% of the cases. However, when doing comparisons at the genus level, >96% of the sequences were assigned to the same genus using either version of the database. Mismatches were mostly due to sequences (actually Amplicon Sequence Variants) which, when tested with Seqmatch had consistently a Sab<0.80 with the best match. Again, the best way to compare studies is to reprocess data based on the same target using exactly the same pipeline, but this is time consuming. Doing comparisons at the genus level is still a reasonable alternative: Article A comparison of bioinformatic approaches for 16S rRNA gene p…
The update version of the last public version of FoodMicrobionet should be shortly available here.

As usual, we are open to collaborations and if you are interested in obtaining data from FoodMicrobionet 3.2.6 contact me.