The causes can be multi-variate and anecdotally, from my own research, microbes (yeast, bacteria, fungi) all seem to play a key role. Anything that disturbs the balance in pathogenic ways can lead to dysfunction, especially antibiotics, but also a lack of plant cell walls in our diets.
Everybody is slightly different, not just genetically, but in terms of the diversity of bacteria.
There have been a few people who have managed to put Crohn's disease into remissions with raw kefir produced at home (the ones at store are not comparable) as well as with Visbiome, a probiotic produced in the lab with many studies behind it. And I've also heard the carnivore diet for short durations may help.
There doesn't seem to be a consistent way to treat Crohn's disease and obviously, medicine to control flares is a must if the situation demands it.
It does seem like a great many gut and autoimmune issues are somehow related to the diversity of microbes though and I look forward to more clinical research like this.
We need all the help we can get.