you are eligible if you have 50% in graduation. Eligibility Criteria (Qualifying Exam) is
Pass with 60% aggregate marks in Bachelors degree (Applied Medical Science or Medical Science and Allied Medical or Agriculture or Nanotechnology or Biosciences or Life Sciences or Food Sciences or Veterinary Microbiology & Parasitology or Genetic Engineering & Biotechnology or Public Health & Allied Sciences or Plant Science) or equivalent, subject to qualifying entrance exam. The best colleges in India providing M.Sc in Microbiology are: Fergusson College, Lovely Professional University

Bharath University, Chennai
Devi Ahilya Vishwavidyalaya
Jiwaji University, Faculty of Sciences & Faculty of Life Sciences
Delhi University
Christian Medical College, Vellore

If you explain the particular University to which you want to get admission for M.Sc in Biotechnology or Biotechnology then I can help you better about teh admission eligibility for the programme.

Good Luck!