I saw this today, and it was pretty easy understand.
"How can bacteria affect our immune system?
The most important way that bacteria affect our immune system is by providing chemical signals that make it slow down once an immune response has been generated. Normally, when you think of an immune response, you think about getting an infection, and then the immune response revs up. But once the infection is gone, the immune response keeps going unless something stops it. That's how you get this widespread problem of chronic inflammatory disease. The microflora don't play much of any role in what makes the immune system start, but they do play a role in what makes it slow down."