Antibiotics May Kill Off Healthy Bacteria in the Gut

November 17, 2008

In the current study, Dethlefsen and his team used a technique called pyrosequencing to take a microbial head count from the stool samples of study participants before they took a short course of ciprofloxacin; then researchers took four more samples over the following eight months. The technique involves reading a specific section of genetic material from every one of hundreds of thousands of microbes, making it possible to identify many of the thousands of different organisms present in the gut and determine their relative abundance.

The researchers spotted up to 5,700 bacteria types in each person before the antibiotic was administered. After the volunteers took Cipro, the gut-bug populations looked a lot different. Overall, 30% of the bacterial types showed dramatic changes in their population. One volunteer in the study had an 82% reduction in the diversity of his gut microflora; one had lost 63%; the third had lost 36%.

However, within four weeks, study participants’ gut bacteria diversity was back to normal.

“That the community can be severely perturbed and then bounce back is very encouraging,” notes Dethlefsen, adding that the findings show there’s probably no reason for healthy people to “freak out” about the effects of antibiotics on their digestive systems. The fact that the volunteers had no digestive problems despite the profound alteration in their gut bacteria suggests that other bacteria took over the jobs of the missing bugs until their population rebounded, he explains.

Still, the health effects of obliterating certain bacteria with a short course of Cipro—which is generally considered to have a relatively benign effect on digestive system bacteria—are unknown, Dethlefsen says. None of the bacteria that were wiped out, or whose populations were sharply reduced, have any known effects on human health, he adds.

“To me, this looks like a very early step in a whole line of research that can really help us understand what are some of the driving forces in developing antibiotic-related diarrhea, in general, and C. difficile, specifically,” says Marya Zilberberg, MD, a professor at the University of Massachusetts, in Amherst, whose research has helped show that C. difficile infections are becoming more common—and more deadly—in the United States.

Next: Why you should use antibiotics only if you truly need them

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