Hello,
This all depends on your interest, if you want a deep knowledge about microbes, pathogens then you must go for microbiology. But if you want application based knowledge about biology then you should go for biotechnology. Also microbiology is a very specific area and biotechnology is really vast of which microbiology is a part. 
Can say that biotechnology has a greater scope than microbiology due to its increased use.
And you can do BTech and BSC in biotechnology but you can only do BSC in microbiology.