[alsocasey]

2) What actually causes "disease"? This implies to me that germs per se are not really the explanation.

IBS (and Crohn's, which is really just a type of IBD), is an immune disorder characterized by chronic, uncontrolled inflammation. All the disease's symptoms stem from this state, so the specific germs involved may or may not be all that important, the body's reaction to them is. When you get down to it, many disease states are just a consequence of regulation of inflammation failing at a critical location.

[bmm6o]

That's essentially the defining characteristic of a "syndrome". It is predicated on the condition or symptoms and not on the underlying cause, which isn't always known. As knowledge grows, more specific diseases can be removed from the classification.