Hey, this one is right up my alley.

To start off, there are different types of proteins, fast digesting and slow digesting. If he has flatulence all throughout the night, he's probably ingesting slow digesting protein powders.

Now the fun stuff. The most popular type of protein is Whey protein and then Casein protein after that. I did an E95 test a few months ago and found that a few foods that my body found inflammatory. The main one among them being anything that comes from cows (i.e. milk, cheese etc) with When protein and beef being the highest offenders. If I consume anything with cow products, be it beef or milk products, my stomach bloats up within 30 minutes and I start being flatulent. The test is a bit expensive, and requires 2 vials of blood to be sent to a lab. PM me for more details.

Anyway, I've taken away whey protein and switched to plant based proteins and I don't have a problem anymore. They taste a bit gritty at first, but you get used to it. I get this one from Costco http://www.leanfit.com/completegreen-protein/ and it's decent. It is about 63% protein instead of Whey which is usually 70-80% protein per scoop. Also check out this post on reddit: https://www.reddit.com/r/Fitness/comments/3l6850/amazon_vegan_protein_powder_price_comparison/ Check out the first comment as well on someone who did a custom mix. i tried the custom mix and it was quite good. Don't get the rice protein by itself as it is atrocious.

Additionally, if he has a gut problem, eating yogurt with probiotics might not be as benficial as it would be a drop in the ocean. I'd suggest seeing a naturopath for all he knows, dairy might be something that is inflammatory to him.

Basically you want him to avoid inflammatory foods and at the same time, get his gut healed. Hope that helps.