An article in the Journal of Obesity in December 2015 clearly links antibiotics to weight gain and the the theory is that the antibiotics permanently change the bowel flora. http://www.nature.com/ijo/journal/vaop/ncurrent/abs/ijo2015218a.html
“Antibiotics at any age contribute to weight gain,” said Brian S. Schwartz, a physician and epidemiologist at the Johns Hopkins Bloomberg School of Public Health and lead author of the study. http://www.wsj.com/articles/study-links-antibiotics-with-weight-gain-in-children-1445451135
In this study, children that took multiple courses of antibiotics during childhood were significantly heavier then those that did not.
What is concerning about the study is the effects are permanent and cumulative
This is not a new and novel theory and has been used in the farm industry for years to fatten up animals and has been reported before.