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This new research seems to think so:

From the original research:

Early evidence from my lab and others hints that, sometimes, our friendly flora never fully recover. These long-term changes to the beneficial bacteria within people’s bodies may even increase our susceptibility to infections and disease. Overuse of antibiotics could be fuelling the dramatic increase in conditions such as obesity, type 1 diabetes, inflammatory bowel disease, allergies and asthma, which have more than doubled in many populations.

Maybe they mean Type 2 Diabetes...

From the Wired article:

Among the findings he cites in support: The population-level observation that the incidence of infection with H. pylori, the bacterial cause of gastric ulcers, has declined over decades just as the incidence of esophageal cancer has risen. In addition, he offers his own research group’s observation that children who don’t acquire H. pylori are at greater risk of developing allergy and asthma, and their findings that eradicating H. pylori affects the production of the two hormones, ghrelin and leptin, that play a role in weight gain.

Our old friend Leptin makes an appearance, even.

What is everyone's experience with weight gain and antibiotics? I've never had any weight problems (BMI <20, effortless ectomorph), and I've taken antibiotics only a few times during my childhood and never as an adult. n=1, blah, blah, I know, but interesting. I do, however, have a host of digestive issues that have developed in my 20's, so my gut flora could be compromised.

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I think they know what type of diabetes they mean. – Jay Aug 27 2011 at 14:40
Both type 1 & 2 are up, and also type 3 if you consider Alzheimer's as such. – Karen Aug 27 2011 at 17:00

2 Answers

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Having reviewed some of the mouse literature, when they use MEGA major antibiotics in combos they would seldom use in humans to kill the gut flora, only about 10% is killed, and in many cases the previous colonies re-emerge doing okay two weeks after antibiotic use ends. I wouldn't promote willy-nilly use of antibiotics, but I wouldn't end up in the hospital with a kidney infection after refusing a bit of levaquin for a UTI, either...

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This sounds like apocryphal evidence. "Sometimes" in "my lab" is pretty vague, and it's not worth my $32 to find out any more.

Obesity results from easily digesting massive portions of food. If antibiotics kill gut flora, you'd expect an epidemic of starvation.

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