This is a bit like asking what you should major in. What are you interested in? Microbiology is a vast field. Do you like medical, environmental, or industrial microbiology? Are you more interested in eukaryotes, prokaryotes, or viruses? Do you need to do laboratory research? If so, what are the limitations imposed by the available equipment?

Try to look for AIDS cure 😉 Currently some czech scientists came up with something new (I guess last shot, before Czech Academy of Science will go down, but never mind), so you can continue with that 😉

As you will probably need some advisor, what about to start with something, what is available at your Uni? 🙄