We don't even talk.
No matter. Just wait until you know he's chowing down, and go into your room. Give him a minute to get going, then come out and ask what the noise was. When he inevitably says "I don't know", hover around for a bit until he starts eating again. Burst out laughing and exclaim "It's you! I thought there was something wrong with the (take your pick, ie plumbing)! Sorry!"
He should be suitably embarrassed. Won't guarantee he'll stop, but at least he'll be a bit more self conscious of it.