Let me preface by saying that I am not an immunologist. My understanding of the GI immune system of the colon is that it is meant to manage pathogens/threats not destroyed by the stomach or small intestine. We are not left defenseless without the colon. As caustic as our GI contents are and as quickly as they move through, threats are generally destroyed or washed out. We have immune system networks behind the upper GI system, too. The colon needs the more complex immune system because of its size, long transit time, and low acidity.
Yeah.........what she said!!
Ok, seriously.......NWO makes a great point. The colon is part of our immune system, but it's really a seperate immune system for the gastrointestinal tract, not really a contributor to the rest of our immune system that's responsible for the rest of our body, minus the GI tract. Our complete gastrointestinal tract, from our mouth to our ass, is really not that well understood, despite what you read. It's almost a seperate entity that lives in our body, as it has its own nervous system, its own control center in the brain and its own immune system. So like NWO says, without a colon you don't need the immune system it provides for itself. What would be much worse would be to have a colon and not have its immune system active. That would be trouble.
The simple way to check your immune system is to have the lab do a CBC and look at your white count. Your white blood cells will tell you if things are amiss or not. Drilling down a little further have them check your immunoglobulins (igG, igM, and IgA). If you're concerned about inflammation have them check your C-Reactive Protein (CRP). You can learn a lot about your immune system with some simple blood tests.