Which database should I choose?

Hi @MichelaRiba, sadly there have been quite a lot of changes in the last 5 years with regard to microbial taxonomy. Each curated database can vary, and use different nomenclatural rules.

Fortunately, we've made it easier to import a few via various QIIME 2 tools and the RESCRIPt plugin. Aside from SILVA, you can make use of:

  1. RDP
  2. GTDB
  3. GreenGenes2

RESCRIPt also has some tools by which you can compare these.

-Cheers!
-Mike