Could Antibiotics Permanently Kill Helpful Gut Bacteria?

Could Antibiotics Permanently Kill Helpful Gut Bacteria?

Most people know that taking an antibiotic can kill off your helpful gut bacteria. Which is why conventional wisdom has it that you should eat yogurt during and after a round of antibiotics. But what if yogurt doesn't go far enough? What if persistent antibiotic use is permanently killing off our helpful gut bacteria, leaving us vulnerable to a lot of serious diseases?
Wired Magazine features an article profiling the scientist behind "a provocative editorial" in Nature regarding this thesis. Martin Blaser argues that antibiotic use (overuse) can cause a permanent disruption in the balance of our gut bacteria. And furthermore that the lack of helpful gut bacteria can be responsible for "obesity, type 1 diabetes, inflammatory bowel disease, allergies, and asthma." All of these diseases have mysteriously been on the rise in recent decades. Can our penchant for antibiotics be to blame?
(Not mentioned in this article is the effect of antibiotic usage in the meat and dairy industry. A chronic low dose of antibiotics from factory farmed meat surely can't help matters, can it?)
There are a lot of studies cited in this article and in Blaser's editorial, most of them seemingly high-level population studies. But these can be tricky to interpret at best. For example, the article cites a study which correlates the fact that infection with H. pylori bacteria has declined over the years, while rates of esophageal cancer have increased. That's interesting, but so what? You may as well blame the increase on esophageal cancer on the rising rate of joblessness, or the increasing price of hay in the Pacific Northwest.
This article also feeds into the "hygiene hypothesis" in an interesting way. Proponents of the hygiene hypothesis would have us stop washing our hands for the greater good. But what if the problem isn't clean living and lack of exposure to filth, but taking too many antibiotics, especially at an early age? Forget demonizing triclosan - our guts are already wastelands thanks to the antibiotics we took when we were kids.
The real answer isn't to wring our hands over the state of our gut bacteria. When kids get sick, doctors will give them antibiotics. Wouldn't have it any other way! What we really need to do is move forward with ways to repopulate our guts with helpful bacteria. This can't really be too hard, can it? I expect the new supercharged yogurts will start hitting the store shelves any day now. Bring on the Mega Activia!