ATG16L1 is one of the genes that can give you a genetic predisposition to CD
ATG stands for autophagy, they've discovered recently that autophagy is very important to handle intracellular bacteria
this study looked at what happened if that ATG16L1 variant was confronted with salmonella
That doesn't mean salmonella is really important in crohn's disease though, bacteria that are likely exploiting ATG defects in CD would be AIEC and some others that are intracellular, maybe listeria, yersinia, MAP (all the mycobacteria really), etc
Intracellular means it's gone inside the tissue of the intestinal wall, in epithelial cells, and in regards to AIEC, in macrophages. All immunodeficiencies point to exploitation by intracellular bacteria, not gut lumen content like the gut flora.
That doesn't mean the gut flora isn't involved in some way, but it seems very far fetched to me that the gut flora is causing transmular inflammation in the intestine, it's likely a bacteria that made it inside tissue (maybe through peyer's patches), can't be cleared because of immune defects, and is causing non-stop inflammation. Just like intestinal TB, which coincidentally looks a lot like Crohn's disease, unlike UC, which looks nothing like crohn's disease.