10,000 germ species live in and on healthy people - Yahoo! News

From the article:

"These bacteria are not passengers," Tarr stressed. "They are metabolically active. As a community, we now have to reckon with them like we have to reckon with the ecosystem in a forest or a body of water."
Our bodies are thought to be home to about 10 bacterial cells for every human cell, but they're so small that together microbes make up about 1 percent to 3 percent of someone's body mass, explained Dr. Eric Green, director of NIH's National Human Genome Research Institute. That means a 200-pound person could harbor as much as 6 pounds of bacteria.
Those bacterial genes produce substances that perform specific jobs, some of which play critical roles in the health and development of their human hosts, said Dr. Bruce Birren of the Broad Institute of MIT and Harvard, another of the project's investigators. Genes from gut bacteria, for example, lead to digestion of certain proteins and fats. They also produce certain beneficial compounds, like inflammation-fighting chemicals.
Given the information in the article, why should anyone be surprised when overall, human's immunity systems are surprised? Perhaps the almost compulsive avoidence of germs and the overuse of antibiotics has something to do with it?

Antibiotics target bacteria. Antibiotics will kill both good and bad bacteria. Other chemicals (drugs, crap processed foods, etc) added to our bodies, dont' help the problem.

The hygiene hypothesis puts forth the idea that they more we strive to be clean, avoid any germs, the less resistance to germs our bodies have. Over cleaning, over use of chemicals, etc, weaken our bodies and when they do come into contact with harmful germs, our bodies have little resistance to them.

Dirty kids are healthy kids - the Hygiene Hypothesis

Sounds pretty primal to me