See for most of the colleges you have to go for entrances. Also there are some universities which offers admission on the basis of merit. But you should always know that getting chance of merit in any good college is very tough so you should prefer for entrances.

Some of the well known entrances are (some of this are Integrated PhD exams and some are for MSc):

• MSU Baroda
• UoP
• NCBS
• NIV
• IISER
• TIFR
• JNU

Some of the colleges offering Microbiology are:

Bundelkhand University, Jhansi

Chhatrapati Shahu Ji Maharaj University, Kanpur

Sri Venkateswara University, Tirupati

Dr Shyama Prasad Mukherjee University, Ranchi

Dr Shakuntala Misra National Rehabilitation University, Lucknow

For more colleges visit the link provided below:

https://university.careers360.com/colleges/list-of-microbiology-and-virology-universities-in-india?ownership=Public/Government&degree=M.Sc.

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