I would probably choose to study bacteria, as I know more about them, and we’ve already got thousands of clinical bacterial sequences that need to be analysed – the methods are still trying to catch up with the amount of sequencing going on! However, there’s no reason why you couldn’t do both. I primarily work on viruses, but a lot of my methods are also applicable to bacteria so I get to work on them too.
Well I picked Viruses 🙂
But if the choice was between the two I think i might go with fungi but this is just because when i was an undergraduate student we had a brilliant lecturer in fungal biology and he really got people interested.
I think either way would be fascinating though as they both cover entire kingdoms (and you could say bacteria are 2 kingdoms) of life so really there would be so much to cover you would never be bored 🙂