Species Level Assignments with SILVA

Hi all,

I've been doing some reading about how the 16S V3-V4 primer set isn't great for species-level assignment, and in the RESCRIPt paper it mentions that "SILVA only curates the taxonomy to genus level but provides the “organism name” given to the sequence in the NCBI GenBank source data, and hence genus–species mismatches can occur."

What about the 18S V9 primer? I've seen papers use the SILVA database for 18S (and some assign to species), but can it be trusted to the species level? I'm focusing on eukaryotic plankton communities with this primer set.

Hi @areaume,

The "species labels" are just a feature we added as part of the RESCRIPt plugin via the --include-species-labels option of get-silva-data. We warn about this under the Species-labels: caveat emptor! Expandable menu in the tutorial.

Although the organism / species labels are present, these labels are not validated by SILVA. At least, as far as we are aware. That is not to say that all these labels are wrong, but quite many do not make sense. Also, there are many cases in which even having the full-length 16S rRNA gene can not disambiguate between species, and sometimes even between genera!

I often will manually BLAST a few sequences to be sure they hit the species I am interested in.

Here are a couple other manuscripts on the topic:


Thank you for the info and sharing the papers!