Marliss,
I agree that some of the observations in that article are a little short of being newsworthy,
(yep, antibiotics do seem to affect gut bacteria, and the outcomes of the roles that they play in our health), but the quote that you listed, reminds me of the old saying, "It's not nice to try to fool mother nature". Of course, they're trying to fool mother nature every time they administer an antibiotic, but trying to take that a step or two further, by manipulating bacteria in order to control their roles in our health bothers me a lot, since that's not really very different from the concept of genetically modifying organisms - it accomplishes the same basic goals, by using a different mechanism.
As demonstrated by the promotion of probiotics, (and the resulting erratic, unpredictable, and generally poor response rate), medical science in general doesn't know nearly enough about any of this stuff, to be talking intelligently about it, let alone trying to use it to modify someone's health. Turning those guys loose to fiddle with such things, strikes me as a little like allowing kids to play with dynamite - everything is fine, until something goes wrong.
The problem is, history shows that virtually all breakthrough medical discoveries are made by accident, not intentionally.
Tex