Approximately 421,000 different types of bacteria can be found on shoes, according to a 2008 study by the University of Arizona. Of the shoes examined in the study, 96% of them were found to have coliforms, a bacterial indicator of the level of sanitation of foods and water that is also universally found in feces of humans and warm-blooded animals.
In addition, 27% of the shoes were found to have E. coli along with seven different kinds of bacterias. Among them are Klebsiella pneumoniae, a bacteria that causes urinary tract infections, and Serratia ficaria, a bacteria that causes respiratory infections.
There is evidence that some modern homes can be too clean and that exposure to dirt can improve children's immune systems. The problem is that not all bacteria are created equal. Some bacteria can be really bad for you. It's a difficult balance to strike, but removing shoes at the door will deal with the worst of it.