OTU taxonomy at higher ranks

Hi all,

My question related to the different ways that taxonomy can be written for OTUs that cannot be classified to genus or species level.
The output below was generated by assigned taxonomy to Deblurred sOTUs using feature-classifier classify-sklearn and the pretrained gg-13-8-99-515-806-nb-classifier.qza model.
Could somebody please shine some light on why the taxonomy name format is different between the two sOTUs? My assumption is that one is because the classifier cannot classify to a lower rank based on limited resolution in the V4 region, and the other is because the taxonomy wasn't provided below family level when the classifier was train?
My questions are:

  1. Is that assumption correct?
  2. If correct, then which is which?
  3. If incorrect, then what is the difference?

Thank you in advance for any insight,

sOTU_ID Taxon
sOTU_22997 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae
sOTU_37411 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__

Hi @cazzlewazzle89 ,
Thanks for very nicely organizing your questions :grin:


This one could not be classified below family level. There were hits to multiple genera, so the genus-level taxonomy could not be resolved with a sufficiently high degree of confidence:

but then this was simply does not have genus or species annotations in the reference database. You can tell because the empty rank labels indicate the annotations in the database (which have these placeholders at every rank, whether or not the label is there):

good luck!

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Thanks a mill @Nicholas_Bokulich

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