Yes these are normal bacterial genera, it seems as an environmental sample.
Thanks，but I dont know why Burkholderia,Caballeronia and Paraburkholderia classified in a same Genus" Burkholderia-Caballeronia-Paraburkholderia"? Because Burkholderia,Caballeronia and Paraburkholderia more like three genera. How How can I explain this genus? Because it the most abundant genus in my result.
I hope this article will help you
What about if you try with Silva 132 version?
I will try it with Silva 132 version, thanks.
all the best
when you assigning taxonomy with 'classify-sklearn'
try to make the confidence more than the default
e.g. --p-confidence 0.9
Thank you for your advice. I really overlooked it
Why? This will not address @YuZhang 's concern, it will most likely just lead to shallower classification. I would not advise increasing the confidence threshold so high for 16S reads.
there are too many associated sequences,I think it is a little difficult to blasting them on NCBI . So is there an easier way? Perhaps should I change the silva to greegenes?
Thanks, but I check it on the SILVA Browser, which you posted. But it didn't solve my problem, these also occurs.
So,what is uncertain placement?
Again, as @Nicholas_Bokulich already mentioned:
That is, the taxonomy
Burkholderia-Caballeronia-Paraburkholderia is not due to the classifier, but the way the reference sequences are annotated within the SILVA database. As you've just proven to yourself, through the SILVA website . Currently, QIIME 2 / RESCRIPt does not alter taxonomic annotations.
Uncertain placement , better known as incertae sedis , basically means that curators of taxonomy are uncertain as to which group an organism belongs. This can be tricky as taxonomic groupings are continually being updated and revised, as @timanix referenced earlier in this thread. There are a variety of ways to represent uncertain taxonomic placement, and they can vary within and between reference databases.
I just add that I also found some strange things (or even true, inexplicable errors) using the last version of Silva taxonomy. Perhaps we should make some kind of warning directly to Silva, my collaborator and I are trying to do so. I invite everybody to do the same, so perhaps they can improve their taxonomy checks.
Better to use Silva 132 at the moment.
Thanks for the input @claudia.vannini
Just to clarify, was this with version 138 or 138.1? I belive they caught some errors in 138 and released 138.1 as a patch.
Out of curiosity, what are the errors you observed? Are these also uncertain taxonomic placements?
Hi, I don't know exactly the Silva version, I'll send the link to this discussion to my collaborator, so that he can reply. The error was a taxon name (a family) that really does not exist (not even ever proposed by anyone).
You might be observing a propagated taxonomy? That is, any empty ranks are filled in with ranks from above. Reasons for this are described in the following threads:
Hi, thanks. No, this is not the case. It's just apparently a completely invented family name.
Please let us know the name, now you sparked my curiousity
It might also be that SILVA has also adopted the GTDB taxonomy as of release 138, so some unofficial taxonomic names might appear in that version (the adoption of GTDB taxonomy is described in the SILVA faqs that @timanix linked above).
You might also be interested in this paper, as a discussion of such unofficial names appearing in taxonomic databases: Microbial Taxonomy Run Amok
If you want a version of the database without these names, I recommend checking out SILVA 132, which was pre-adoption of GTDB taxonomy... RESCRIPt can be used to compile a QIIME 2-compatible database for that release as well.
Hi again. The apparently invented family name is "Fokiniaceae". As far as I saw, this name does not appear in the GTDB taxonomy. It's a bacterial group we know well, the family should be Midichloriaceae (which indeed does exist in the GTDB taxonomy). The genus "Fokinia" exists (within Midichloriaceae), but not the family Fokiniaceae. No idea of the explanation.
Yes, as I wrote, I think SILVA 132 could be a better choice for the moment.
Interesting... indeed this appears to exist in SILVA 138.1:
However, it does also exist in the GTDB taxonomy, as of R89, but not later releases:
In later releases of GTDB it is corrected to "Midichloriaceae".
So this is probably an issue of SILVA adopting the GTDB taxonomy but being slightly behind the latest GTDB release...
Thank you very much for the check, yes it's probably as you say....they corrected the error in the latest release of GTDB but SILVA is still behind...
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