You are doing your 2nd year B.E and it is quite understandable that you joined the course after completion of XII/10+2 with maths, Physics and Chemistry as optional in plus 2. It is quite astonishing to note that you are interested in Microbiology and wanted to shift after completion of 2 years in a B E course to B Sc (Microbiology), a three year degree course. Think twice. You could have given a thought before joining your B E course and note that valuable two years are wasted, if you want to shift to a new course of your choice. One should not be haste in taking decisions about a glorious career at a belated stage. Engineering is a good choice with more options of your future as you have already completed two years (though you haven't specified your branch of study) and I don't suggest to go for B Sc (Microbiology) now as an expert advice.
Coming to the point, if you have done your XII standard with MPC group, you can't shift to B Sc (Microbiology) after discontinuation of your B E course. Microbiology is a study of science of Microorganisms, cells including immune system and immunology. Thus it basically forms part of Biology. If you have done your XII standard with MBiPC (Maths, Biology, Physics and Chemistry), then you can have a choice to opt for it. Nowadays, some colleges offer such courses for MPC students also but it depends on the reputation of the college. B Sc (Microbilogy) as of now not career fetching and you have to do your Post Graduation for betterment of your career. It is upto you to decide but I strongly suggest you to continue your B E course as two years only are left and Engineering has good prospects as compared to this field.