Hi,

Engineering in Biotechnology is a new upcoming field so PG will also be on the same lines. I dont see specialization in Microbiology in many M.Tech courses.

Alternately you could do your B.Tech Biotechnology and apply for IISc BAngalore's integrated PhD. Now they have a dedicated Microbiology dept. and the eligibility also allows for B.Tech biotechnology.

If you ask me there are very few choices of doing a PG course in engineering with Microbiology as it is mostly offered in M.Sc courses. Better to look at integrated PhD courses. they have better scope.