Differences of unassigned, unidentified, uncultured taxa.

Hi Everyone!

I have ran 16S RNA sequences to DADA2 (ASV) and SILVA 99% to get my taxonomy table.

rela_asv.tsv (82.0 KB)

I understand that empty cells (green) are those that can't be assigned on the level.

But I'm not sure what "uncultured" or "unidentified" (blue) cells are.
Are they certain species that are not named yet?
Or can I also regard them as unassigned empty cells?

I'm very new to this field, teaching myself, and currently don't have any supervisors.
Any comments would be very helpful for me.

Hi @rosebae,

Yes! There are a lot of sequences that are unnamed in our databases, and so labels like "uncultured" or "unidentified" holds space for that. Different databases treat these differently; but for Silva, this is how they're labeled.

I would say you have a taxonomic assignment and pretty good name, so its not the same as a fully unclassfied. Personally, I tend to extend "unclassified" or something into the taxa that were unclassified (I think you might be able to do this in RESCRIPt, but I'm not sure), so the blanks genus name would be "g_uncl_f__Oscillospiraceae". There are a number of ways to describe these in the text ("uncultured genus from family Oscillospiraceae" vs "unclassified ASV from family...")