Hi there. 

Both the subjects of Food & Nutrition and Microbiology are great and have immense scope and booming market. 

You will have the opportunity of doing both lectureship and research in both the subjects.

With food & nutrition you can become a licensed Nutritionist and have your own private practice. Hence, there's more Independence and freedom here. 

Moreover, people these days are becoming very conscious of their health and diet hence the future seems brighter from this side. 

Furthermore, I'd advice you to go through the syllabus of both the subjects, talk to seniors, collect some more information regarding both and then choose wisely. 

Hope this helps.