I could suggest to work upon improving the shelf life and storage period, shorter fermentation time, and enhancing the flavour of any food product of your choice.
You can read upon the available literature to find out out a hot topic of your interest, analyze the gap and work upon it.
Despite much approached in many research papers and experiments, the area of cheese maturation is still a very challenging research field and far from finding its solutions. The economical interest in reducind the cheese maturation time is very high if think that even 2-3 years are required to get a high quality maturated cheese. The same economical and market interest could be shown for wine stabilization and maturation. These two directions seem fairly old but they could offer new or better solutions if look to discover and select new enzymes, proteins or try innovated technologies.
Plenty of things can be done on fermentation, but it depends how much time you are having. I would suggest a few of them,
1. Dynamics of the fermentation process- how the microbes are changing with fermentation period as well as the physical and chemical changes in the substrate.
2. Isolation of microbes from the fermented product and looking for their applications like probiotic properties, production of a particular product or some health benefits.
3. Optimization of the fermentation - The existing fermentation process can be further standardized to make it more easier and new starters can be developed using potent microbes.
4. The probiotic microbes isolated from the fermented product can be used for study of certain properties like adhesion to intestinal cells using cell culture technique.
Since you indicated interest on pre/probiotic; I suggest Development/improvement of the pre/probiotic properties of a named fermented product (which may be a dairy product; a fermented legume product; e.t.c). The project will involve establishing the pre/probiotic potentials of the product; improving the fermenting organisms potentials for production of pre/probiotics;( this aspect may involve genetic improvement); evaluating the level of improved pre/probiotic potentials of the organisms as well as the products.
I could suggest something about microalgae, in particular the usage of microalgae as probiotic compounds. I know that they have high nutritional quality and they can be used as food supplement.