We recently used QIIME2 to perform bioinformatics analysis on the results of PCR amplification and sequencing of 16S rDNA, and I found Daphnia_magna as one of the species assigned as shown below:
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium;s__Daphnia_magna.
Please help me. I have read much about Daphnia_magna as a small planktonic crustacean but I don't understand why it is assigned this way. Among the known species of the genus Flavobacterium, the closest name is F. magnum. Please what could be wrong? Is there a Daphnia_magnum that is a bacterium?
Hello!
I think it is an error in Silva database. You can contact Silva mantainers so they could fix it. I already encountered several times that the source of DNA isolation is mistakenly indicated as a taxonomy in 16S databases.
For 16S analysis, it is better to stay with genus level annotations rather than to work at the species level.
This particular bacterium was likely isolated in Daphnia magna first, yet has not been given a proper name (Daphnia magna is not a bacterium). In the Silva database you often get these kinds of hits; there are various pigs (Suis) in there as well for example. So, it's not really an error of the Silva database though it could be if they by now do have a proper name for this particular bacterium. I recommend simply taking the representative sequence and blasting it to see if you get a Flavobacterium hit that does make some sense.
With 16S analysis it rather depends on which region(s) your looking at and at which genera whether you're able to go down to the species (or even strain level). Various Faecalibacterium prausnitzii strains can for example be differentiated (using ASVs) from one another just using V4.
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