I am seeing multiple OTUS for many bacteria e.g. Prevotella…all ending with a different number at the end. What does this mean…
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 20
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 15
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 17
It is typical to have multiple OTUs/ASVs with the same taxonomy assignment. Just because the OTU/ASV is a unique sequence does not mean that it belongs to a different species, and in fact sometimes these can even be different copy variants within the same strain.
I am not sure where the number at the end of each is coming from — you would need to provide more details of what command produced these strings — but my guess is that this is appearing after you plot these data, since in my experience most plotting software (NOT QIIME 2) adds these numbers on the end to arbitrarily distinguish replicated observation names, e.g., if you are plotting these data as a heat map. In any case, this is nothing to worry about and these numbers carry no real meaning, it is just to arbitrarily distinguish these OTUs with identical taxonomy assignments.
For the record, this is not QIIME taxonomy. QIIME is not in the business of curating reference taxonomies or creating new taxonomy formats. This appears to be Greengenes taxonomy data, except that the arbitrary numbers are not from Greengenes.
I hope that helps!
Many thanks for the quick reply. I have a follow up question… Should we merge all these OTU’s to get one set of relative frequency data per taxonomic assignment. Would you add them (since all of my data adds up to 1/sample).
You are right, the numbers at the end were added when I transferred my data to JMP.
You can use taxa collapse to do the job.
Sounds like that is probably want you want, if you are interested in differences in taxa, as opposed to differences in individual OTUs.
I hope that helps!
Thanks again… this is very helpful.
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