Classifier and taxonomy

[SoilRotifer (Mike Robeson)]

@Dzana_B

just in taxonomy file I replaced level marks to match the rest of the program I am developing. So, I quickly replaced D_0__ with d__, and so on.

You do not want to do this. That old numbered rank system is inconsistent. See here for more details:

Why all taxonomic levels on BarPlot have 'D' letter?

I can likely provide some insight here as I am one of the contributors that helped to format SILVA database for QIIME. The D_X__ convention was chosen to be as much of a unique and “safe” text string as possible, considering many of the bizarre taxonomy text annotations within the SILVA reference database. That is, it was meant as a quick fix to be able to search and parse these taxonomy strings. The ‘D’ was a way of annotating the “taxonomic Depth”. At the time some of the code was written, th…

@Dzana_B

The reason I am not using pre-trained classifier is that I have some sequences blasted, and I was thinking of improving taxonomy at species level, i.e. I blast the sequence of this organism:
D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Clostridiales;D_4__Lachnospiraceae;D_5__Blautia;__

and find that I could add species label to this, i.e. Blautia luti, as it has pretty nice match.

Maybe this is not the best practice to follow, but I would definitely like to improve classification of bacteria in samples at this level.

You can use our RESCRIPt tool to do something quite similar:

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for constru…

@Dzana_B

I cannot find in starting tazonomy file, i.e:

d__Bacteria;p__Firmicutes;c__Clostridia;o__Peptococcales;f__Peptococcaceae; ;

This makes me so confused.

Is that above equivalent to:

d__Bacteria; p__Firmicutes; c__Clostridia; o__Peptococcales; f__Peptococcaceae; g__uncultured; s__uncultured_bacterium

as I found this taxa in the taxonomy file.?

I assume the first taxonomy string is the result of taxonomy classification? If so, there is no easy way to know that classification is indeed equivalent to the second taxonomy string you listed. Well, without looking through the reference sequences anyway.

This issue is that the classifier likely could not disambiguate between the sequence with the taxonomy full taxonomy string d__Bacteria; p__Firmicutes; c__Clostridia; o__Peptococcales; f__Peptococcaceae; g__uncultured; s__uncultured_bacterium, versus several other reference sequences with nearly identical taxonomy (likely different genus and species strings. So, the classifier will return the lowest common ancestor (usually). In this case, it could not determine anything past the family level.

@Dzana_B

Qiime omits “uncultured” word from taxa? Or?

Nope, not unless you filter your sequence data or your reference database in that way. If you see any text after any of the prefixes, e.g. g__uncultured, then that is the taxonomy pulled directly from the reference database itself. RESCRIPt allows you the option of appending the organism name as the species label. However, be careful of trusting this. See the Species-labels: caveat emptor! section of the RESCRIPt tutorial that I linked above for more details.

Hope this helps!