It is a fascinating and clever idea get microbial genomes of your interest separated from a complex community! It basically works by treating the same environmental or community sample in different ways (treatments) and then extract the DNA to further sequence them. Due to the treatment, there should be differences in the microbial abundance in these smaples by which you can separate your interesting microbial bins on a coverage bi-plot (for example).

I have been using QIIME for microbial community analyses for the past 5-6 years! the QIIME community has taught quite a large deal about how to analyse and infer the community data! Their tutorials and debugging strategies always made life easier for biologists like me. I have definitely been a big fan of their project.