taxonomy confusion with s_

In my taxonomy i have this example:

  • k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;__

  • k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__

The first one only got to genus and the second one got to species, however, was not assinged to any species.
Is there a way to know which species it is ? And if not it is ok to show my data this way (consider the last one as a specie)?

Hi @annsantos,
See here:

So no there is not really a way to see which species it is — it is in the reference database but the species label is unknown (probably because multiple species are too similar to differentiate with that marker).

Hi @Nicholas_Bokulich,

I think o got it! So in your opinion, you think i shoul get rid of k__Bacteria_;;; of my data?

Thank you

Yes — 95% of the time these seem to be non-target DNA but I would confirm by grabbing a few of these sequences and seeing what they hit in NCBI-BLAST (exclude uncultured/unknown organisms from the search)


Thank you

How can i do that?

qiime metadata tabulate --m-input-file seqs.qza --m-input-file taxonomy.qza

then search for the taxonomy of interest, copy the sequence, and search on NCBI-BLAST online


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