Hello Aqleem,
Take a look at this alpha diversity guide from the Werner Lab.
http://www.wernerlab.org/teaching/qiime/overview/e
That last graph and paragraph is really helpful.
It looks like the fasted samples had a higher phylogenetic diversity than the control mice microbiomes.
Yep! This is exactly kind of conclusions you could draw from your samples. Is that helpful?
I usually choose a max depth around the lower depths that all my samples cover. So if my samples have 1,200 reads to 112,100 reads, I would choose a max depth of 1,200. Or maybe I would throw away samples under 5,000 reads, then choose 5,000 as my max depth for rarefaction.
Let me know if this helps.
Keep asking great questions!
Colin