I've heard about some study that found that kids who don't play in the dirt and eat sandbox sand early on don't develop the right bacterial flora in their gut and they never end up processing food correctly.
When I was little-little, my mom had a neatnik friend who was obsessed with disinfecting everything her toddler came in contact with. Well, one day, we're all at the park for a playdate, and a fly lands on this kid's lip. Two days later, he's going in to the doctor to get his new abscess taken care of - because he'd never been exposed to bacteria, his immune system was underdeveloped, and his body couldn't fight off the germs from the fly.
I grew up surrounded by pets, running around in the woods, hanging out in barns, and otherwise engaging in the messiest activities I could find. I came home looking like Pig Pen more days than not, but I've got myself a cast-iron immune system.