Hi @fgara,
Glad it helped!
Some of this is anecdotal. I suspect that if you go back to that earlier analysis and look, you'll find a set of specific features that drive that phylum level difference. (It's also worth keeping in mind that taxonomy is nested.). I dont think its a great example of a paper or how to do analysis, but if you look at Table 3 of this study, and you look up the taxonomy associated with each level, you'll find that it's nested and the difference in Fusobacteria is driven by the difference in Leptotrichia. (However, I dont recommend using the paper as an example for much else, I dont think they did a great job with respect to that nesting aspect.)
I think there's also an ecological question - is it important to know that global warming is associated with a change in the number of things with spinal cords 
and the number of things with shells 
, or is it more helpful to know a specific set of species within phylum chordata is driving CO2 and CH4 production :
? I think community level data is really important, don't get me wrong, but Im not sure that collapsing to that high of level works as well as alternative statistics (alpha & beta diversity).
Best,
Justine