Something I thought about is how one doesn't rule the other out.
If P is being infected by MAP, and Q is having crohn's.
Then P ⇒ Q
You are infected by MAP, therefore you will have crohn's.
But the reverse is not true, having crohn's does not mean you are infected by MAP. That's where some are missing the ball I feel, crohn's could be wide range of bacterial infections.
When people say, "I was checked negative for MAP and have crohn's, therefore crohn's is not MAP", they are wrong, because Q does not imply P, but it is still true that P ⇒ Q. You are infected by MAP, therefore you have crohn's.
It would be like saying "I have a broken bone and didn't fall off the stairs, therefore falling off the stairs doesn't break bones"....that is wrong.
It also becomes pretty ridiculous when you realise that so many animals have johne's, we're not talking just cows here, sheep, dogs, cats, there are many animals with johne's. There has to be a human counterpart of this disease, we are not immune to this bacteria, the most likely candidate is crohn's.
We're way past a hypothesis, we know people with crohn's have more MAP in them than "healthy" individuals, the two are related. It doesn't mean that everyone with crohn's has MAP, but the fact is still there that MAP is found in patients with crohn's in much higher numbers than "healthy" people.