Should I go for a Ph.D. in microbiology or Clinical Laboratory Science?

Depending on what you ultimately want to do. The clinical laboratory science will help you gain the knowledge and skills to become certified to work in a clinical laboratory position, which are an area of need right now. Going into the Ph.D. program will lead to better money, but it is a research degree that typically leads to working in a research setting. I just left a Ph.D. program in microbiology because I wasn't as pionate about it as I am another field. With the clinical laboratory science degree, you don't lose much time, but with the Ph.D. program, be willing to put in about 6 years plus at least another 2 for a post-doc position before you can really start a career.