Ever heard of this?
It's still in its testing stages, but it might explain this phenomenon. Even though it's been in literature for more than fifty years, now, Dutch physicians are conducting a mass study, right now. It seems to be highly effective against pseudomembranous colitis which is caused by an overflow of Clostridium difficile in the gut flora with the only therapy being a high dose of Metronidazol or Vancomycin orally. However, a stool transplant from a healthy donor has been suspected of being at least 80% successful compared to like 40% success rate of the antibiotic therapy. It might even work on Morbus Crohn or Ulcerative colitis.
Considering that the gut flora is responsible for synthesizing many different substances, most of which dispersing into the blood stream affecting bodily functions, it seems reasonable that a change in its natural composition (like administering antibiotics) might affect certain aspects of the human metabolism, probably leading to late-onset effects like obesity and metabolic defects.