I do too -- I just have no idea how to actually trigger the fight. I don't know if you have to "use" the item (if so, I can't figure that out) or go to a place (if so, I can't find the place).
There are a couple of Jimbo's hunts that unlock through the story. You can't get to the bacteria until near the end of Day 2. All the items you need were automatically given to you by Jimbo and the Use prompt will let you know you're essentially summoning a boss if you press X (although you can use summons on these hunts, which I recommend for expedience).
Anyway, I personally just finished day 2 myself and man this game is not slowing down a bit. I will say though that I'm already level 14, and as a mage with both fire spells fully upgraded to level 4, a weapon that instantly casts slow and double defense down, and badges that cause every hit from Dragon's Breath to refill my PP bar to full, I am just tanking through this game in ways I'd have never expected. I'm still wearing my level 3 hat and clothes just because of the PP bonuses. I wonder how much more gear strategy is required for other classes, but at this point I've been turning down new weapons left and right for hours now.