Gene therapy for cyborgs

I wondered aloud to a friend tonight:

"How long do you think it will be before people lose their feeling that there is something sacred in nature, and [after the technology becomes available] begin to undertake trivial genetic engineering and electronic modification of their bodies and children?"

This conversation was started with the statement of a fellow grad student that stem cells are being proposed as a vector to introduce drugs and genes into sick patients. It's easy to see powerful near term possibilities (e.g. correcting cystic fibrosis) in addition to ethically worrisome long term possibilities (e.g. increasing height), but my one friend's labmate came up with a new perspective I hadn't encountered before.

In agriculture, humans have been surprised repeatedly (and devastated!) by the unforeseen consequences of genetic modification. Continual selection for yield traits in crops neglects disease resistance traits that are invisible until you really need them. Incorporating a certain cytoplasmic sterility trait into corn allowed great advances in breeding until a fungal pathogen showed up that was able to exploit a subtle weakness that went along with it.

No amount of genomics will completely decode our DNA or explain every function of every gene and intergenic region. So what happens if large portions of our population start adding or removing certain specific genes from their own genomes?

What rare pathogen, toxin, or environmental stress will make its periodic (and formerly unnoticed) appearance after widespread interuption of the obscure genetic element that formely defended us from it?