Bos taurus is everywhere in my 18S SILVA 138 taxonomy!

Hi @16sIceland,

If you notice, the upper-level taxonomy does not fit that of Bos taurus, in fact this is from a fish of some kind. The SILVA database we provide was made using the --p-include-species-labels flag. Which basically appends the host organism name (i.e. usually the organism from which community DNA was amplified from), as the species label. However, the host organism name is not always that of the sequenced DNA.This is outlined in more detail within this forum post.

Specifically, read the warning we have under the under the drop-menu "Species-labels: caveat emptor!" :warning:. That is, SILVA does not currently curate taxonomy down to the species level and we offer the option to append the organism name, as it is sometimes helpful. If you'd like you can use RESCRIPt to make your own reference database without the organism names appended as the species labels. Or you can use RESCRIPt to make your own database from NCBI (see the tutorials on the RESCRIPt page.

It could be that this was a contaminant, or some diet bycatch :thinking:? But the key point is, when observing an odd result like this, make sure the entire taxonomy is reasonable, then confirm via BLAST or other tool. :mag:

Hope this helps!