Hi,

No, you don't need to appear in GATE to do M.Sc in microbiology because Most of the institutions have entrance exams as admission mode.

The top colleges offering M.Sc. Microbiology are:
St. Xaviers College Mumbai
University of Lucknow
The Oxford College of Science Bangalore
Fergusson College Pune
St. Xaviers College Kolkata
Barkatullah University, Bhopal

I hope this helps.
Good luck.