I'd be interested in the answer to this too.
Although my strength is not low noise analog, I would have thought that most of your gains would be through just isolating the bus from the micro (is it galvanic? transformer? optical?) but I don't even know if this is necessary. Presumably, if they are mixed signal parts they are already designed for low noise applications? So you just need to be careful that you use a satisfactory power supply topology. I mean, my DSO is full of digital and analog stuff, and they're even on the same board with no isolation. I've only ever seen serious isolation when a) one side of a connector can't be trusted or b) the instrument is supposed to connect to a person
edit: also c) when one side of the board has a stupendous voltage on it