OTU taxonomic asssignment

Hello All,
Can someone remind me the meaning and difference again between different OTUs assigned like the following:

k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__; s__
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Parabacteroides
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Parabacteroides; s__
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae; g__; s__

Hey @Jen_S,

The two forms of taxonomy strings you are seeing are technically unrelated.

The taxa with trailing ; <prefix>__ are Greengenes OTUs which are specific enough to be considered a “species” or “genus” or whatever, but for which no one has an actual name for. For example:

k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__; s__

represents some kind of species of bacteria, but we don’t have a taxonomic name for it.

The second form, where there is no trailing prefix, happens when you perform assignment via feature-classifier. It will stop classifying at a confidence threshold that you can configure, so it may only have a classification up to family or genus, and so it stops there.

So in that same example, the feature classifier is confident that your ASV is a member of that GG OTU, and so you receive the “full” taxonomic string (which just so happens to not really have a name for genus and species).

Hope that helps!

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