At our institution we have had some debate about this topic. So let me give some background:
Qiime2 produces a OTU table which shows the number of sequences that matched to a specific OTU. It also produces an Taxonomy table which links all the OTUs to their corresponding taxonomic identity.
So what we were discussing was whether to use the number of sequence hits per OTU for alpha and beta diversity, as well as abundance graphs. Or should we use the Taxonomy table and count the number of occurrences for each taxa.
An example of this would be something like the following:
Here are two OTUs:
D_0__Bacteria;D_1__Cyanobacteria;D_2__Oxyphotobacteria;D_3__Chloroplast;D_4__Virgulinella fragilis;D_5__Virgulinella fragilis;D_6__Virgulinella fragilis and
If we used the first approach then there would be, for example, 3000 sequence matches for the first OTU and 1500 for the second OTU. However, they represent two different species from the same Class. So abundance wise, the first OTU could be represented twice as much as the second. With the second approach they would share the same abundance percentage.
What is the correct approach for these types of analyses according to the bioinformatics community?