Hi @didietkeren, if you read my pipeline notes as well as this post, you'll see why I do not trust species-level taxonomy. As far as I know SILVA does not curate the taxonomy beyond the genus level. 
As a result, there will be be potential conflicts with the species labels and upper-level taxonomy. This has been noted by other research groups too, see here. Which is why I made two versions of the reference database, with and without the species label. 
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