Is there any sense in SILVA taxonomy genus names like
“uncultured bacterium”, “gut metagenome”, or they make no sense and for statistical analysis of gut microbiome composition (and further publication) it is better merge all the 3 taxa below:
Unfortunately, these annotations are so vague that it is really unclear what they could represent and if they are theoretically same or separate entities. Given that you are receiving these classifications for distinct ASVs is a pretty good indication that they do represent distinct taxa, but you could look at those ASVs to decide for yourself whether it is worth collapsing. If I were in your shoes, I would keep separate.
Though for your purposes maybe it makes sense to collapse for display purposes (e.g., to reduce the number of unique taxa displayed on a heatmap or barplot) — in which case go for it but note this:
Note: This is actually unclassified at the D_5 level (meaning that the classifier could not determine a confident D_5 classification, as there are many equal matches or no good matches)… the others are classified but to ambiguous taxa, so if you relabel you may want to relabel the unclassified and classified separately, e.g., as:
D_3__Clostridiales;D_4__Clostridiales vadinBB60 group;D_5__unclassified
D_3__Clostridiales;D_4__Clostridiales vadinBB60 group;D_5__unknown