For artificial joints like a hip and a knee joint, you have a lot of exposed materials like titanium, stainless steel, or medical polymer, so it doesn't have an immune system. Getting a biofilm infection forming on an artificial joint sometimes means taking the implant out, even if it's working fine.
So biofilms are a tough problem. They're far more sinister than conventional bacterial colonies. Since this is in the digestive tract, I wonder if some type of detergent can be found that simply dissolves the film matrix, washing away the bacteria and fungi.
And, I guess the biofilm in this case is especially tough. From the abstract:
The mass and thickness of triple-species (C. tropicalis plus S. marcescens plus E. coli) biofilm were significantly greater than those of single- and double-species biofilms.
On the other hand, something like Crohn's means your microbiome is already damaged, or at least not optimized to make a positive contribution to your health. Fecal transplants from healthy donors have shown promise in similar circumstances; if you're interested in treatments for such conditions, that might be a good place to look.