Microbiome can be a complex ecosystem in many ways!
Here, BaseSpace is building your feature table (Im not clear how) and doing feature classification (although Im not sure how). It’s the equaliviant of q2-dada2, q2-deblur, or q2-vsearch, depending on which approach it’s taking and then combining it with q2-feature-classifier. All of those also give you abundance profiles I would double check with Illumina/BaseSpace to be sure you know how they’re getting those identies, it’s important that you know!
…I’m also personally somewhat dubious of species level classifications off most modern databases, particularly with 16S. Collegues of mine may disagree, or may apply filters (if only 1 or my 5 options belong in my site, maybe I can take that resolution). A lot of databases dont provide species level resolution at all, and so I’d be careful pretty careful. Others tend to be somewhat less conservative here, but thats my two-cents.
You can then absloutely pass your feature table from BaseSpace into QIIME 2. You could also pass your feature table from Dada2 in R, from Mothur (kind of), Usearch, UNoise, SortMeRNA, etc. QIIME 2 has the capability to do diversity analyses (q2-diversity) along with differential abundance (statistics!) and a bunch of other shiny things. (Seriously, I recommend the plug in library, 11/10 would use again.)
A lot of people will present these graphs in their publications and discuss them. I (again) like stats so Im a big fan of some of the differential abundance approaches. I also think its important to think about what you need to show and the best way to show it.
On the other hand, you’re working at a community level, and will probably get more milage out of community-level analyses like alpha and beta diversity for your publication. But, the two are complementary IMO and tell you different things.