An intimate study of three women given ciprofloxacin showed the drug suppressed entire populations of beneficial bacteria, and at least one woman took months to recover.
The study, published in the Proceedings of the National Academy of Sciences, supports the common wisdom that antibiotics can damage the "good" germs living in the body.
It may also support the idea behind the development of so-called probiotic products including yogurt with live cultures of bacteria.
The researchers tested the three volunteers daily, giving them a five-day course of the commonly used antibiotic ciprofloxacin twice during the 10-month study.
They ran DNA tests on stool samples from the volunteers to determine what kind of microbes were living in the gut.
"The effect of ciprofloxacin on the gut microbiota was profound and rapid," Les Dethlefsen and David Relman of Stanford University in California wrote.
"By one week after the end of each course, communities began to return to their initial state, but the return was often incomplete."
More and more studies support the idea that humans and other animals have a symbiotic relationship with germs. Microbes in the intestines help digest food and "good" germs can take up space and keep bad germs away.
"The human distal gut is one of the most complex ecosystems on the planet," the researchers wrote in the study, available here
Gut microbes can affect obesity and may play a role in allergy. Lactobacillus reuteri, found in breast milk, may protect against rotavirus infections, other researchers have found.
Several recent studies have found that certain bacteria cause inflammation that can affect appetite as well as inflammatory bowel conditions like Crohn's disease and colitis.
Regularly wiping out the body's bacterial population could also be helping drive the rapid spread of drug-resistant superbugs, the Stanford team said.
"One potential ramification of the altered community is an enhanced carriage of antibiotic-resistance genes in the human population," they wrote.
"Every course of antibiotics may represent another roll of the dice," they added -- potentially a "bad" strain to replace a beneficial species.