I think this film/show was made in the early 2000s.
It featured some sort of bacterial habitats co-existing in a boy's body. The good bacteria would fight off the bad ones, and when they failed, the boy would suffer repercussions, like having a fever or blacking out, etc.
Any idea what this film or show's name is?
I suspect that this is the animated series Ozzy & Drix, which aired between 2002 and 2004.
A spin-off of the live-action/animated hybrid film Osmosis Jones, Ozzy & Drix features Osmosis Jones, a white blood cell, and Drix, an over-the-counter cold-relief pill, as they battle germs, diseases, and other illnesses, inside the body of teenager Hector Cruz.
You may be remembering Osmosis Jones itself, but in the film, they were inside the body of a middle-aged man played (in live-action) by Bill Murray, rather than a teenage boy as you remember, so I think Ozzy & Drix is more likely.
There is another series that aired slightly earlier (~1988) that fits the description: Once Upon a time: Life
It features the different parts of the body, how they work together, how they recognize and battle germs, diseases, cuts and other things.
Most of the series is from the inside of the body, but there are outside views that show the effect of the illness or how they happened in the first place.
