Do a daily transporter sweep for dead organic material all over the ship to purge all those skin cells and hairs and other leftovers of our existing. No more vac
Just avoid areas with life signs. Person in the room? Delay the transporter sweep for an hour and check again. Or alternatively just don't clear dead skin cells/hair/dust within a 2ft radius of a given life sign, and do maybe 3 sweeps a day.