You are comparing two subjects which are different from each other. MSc Microbiology is a course in which you will learn in details about the Microbial systems and there cognitive approaches, identification, characteristics and application in solving real issues. But in MSc MLT you will learn about the improvisation of Lab instruments, manipulating and using them in correct manner in order to achieve the maximum precision, maintenance and troubleshooting. Thus as you can see both are not that much interrelated. Both the fields have enough scope in Industrial as well as medical point of views. Also doing research in Microbiology can be a great option for you if you are interested in it.

Thus in general the main thing which lie is your interest. I would recommend you to go for the course which you are interested in. Both the courses are equally opportunistic and both of them has great employability but you have to choose the one which satisfies your target.

To know more about MLT visit the link below:

https://www.careers360.com/courses/medical-laboratory-technology-course

To know more about Microbiology visit the link below:

https://www.careers360.com/courses/microbiology-course

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