"The first study, published Wednesday in Nature, used mice to investigate the effects of low doses of antibiotic treatment. The researchers, led by Martin Blaser, thereby mimicked the treatment farm animals have been receiving in the United States in recent decades. Since the 1950s, low doses of antibiotics have been widely used as growth promoters in animals, reportedly increasing their size of by up to 10 percent." 

"Aiming to explain these observations, Blaser's team treated young mice with low doses of antibiotics and found that while the treated mice did not become larger overall, they were, in fact, more obese." "Overall, the scientists concluded that the treated mice had bacteria that were more efficient in digestion."  

The conclusion of study one is that bacterial shifts due to antibiotic use change the overall metabolism of the bacterial organisms and then the mouse as well.

"The second study, published in the International Journal of Obesity this week, aimed to corroborate these findings in humans. The research led by Leonardo Trasande looks at statistical data collected from nearly 11,000 children in Avon, England. The researchers found that children, who were given antibiotics in their first six months, had a higher incidence of obesity later. The difference was most pronounced at about 3 and tended to teeter off at about 7, the latest time analyzed. Obesity at that age correlated slightly with antibiotics during the toddler stage."

The overall conclusion is that we are altering the good bacteria of our intestines to our detriment.  To date we have good data that causes of gut dysfunction and therefore metabolism dysfunction are occurring by these mechanisms:

1) Cesarean sections

2) Not breastfeeding

3) Early and frequent antibiotic use

4) Early antacid use

5) High refined grain diets

6) High saturated fat diet