Your child with severe dysbiosis needs to have a completely organic diet with no processed foods, even organic ones. I'm sure you know that. His water needs to be un-fluoridated. The GAPS diet is great if he is suffering from bloody diarrhea.
The thing that helped my dysbiosis the most was eating two stewed apples a day for longer than 10 days. Cook green or other tart apples with a couple of tablespoons of water and use a potato masher to crush them into chunky applesauce. Make sure to leave the skins on. I make about 5 days worth at a time and store in the refrig. It makes a nice breakfast. If my stomach got upset, I ate some more the same day. If your son can handle it, add some cinnamon and raisins.
Our gut needs a healthy biofilm. Biofilm is composed partly of cellulose. You get that from the pectin in the apples.