See there are quite a good number of colleges in India for PhD Microbiology. But if you want to know the best according to me. I would say you should go for NCBS-TIFR. The institute will avail you a great research facility as well as research opportunities most probably the best in India.

Now rather than this you can go for IISc or IISER BHOPAL for some of the great research projects. But always keep in mind that no institute will give you as much exposure as NCBS(IISC also gives a good exposure).

I hope my answer helps. All the very best for your future endeavors!