The human gut is home to a galaxy of bacteria thought to protect us from disease in the digestive tract and beyond. So what happens when we take antibiotics?

Sure, the pills can wipe out bad bacteria. But they also kill the good stuff. On top of fueling a rise in antibiotic-resistant superbugs, they could be permanently changing the gut environment — a feat some experts fear might be making us fat.

Dr. Martin Blaser of New York University Langone Medical Center studies the effects of antibiotics on Helicobacter pylori — a bacterium that lives quietly in most but leads to ulcers in some.

Although the majority of H. pylori infections are harmless, doctors are quick to treat them with antibiotics that change the way the stomach works.

“Antibiotics are miraculous,” Blaser told ABCNews.com in August after publishing an editorial on antibiotic overuse. “They’ve changed health and medicine over the last 70 years. But when doctors prescribe antibiotics, it is based on the belief that there are no long-term effects. We’ve seen evidence that suggests antibiotics may permanently change the beneficial bacteria that we’re carrying.”

Blaser discussed his latest research with the New York Times, explaining that antibiotics for H. pylori trick the body into eating more by disrupting hunger hormone levels. Indeed, mice given antibiotics get fatter than their untreated counterparts despite having the same diet, Blaser said.

The findings add weight to studies that have found differences in gut bacteria between lean and obese mice. Changes in gut bacteria – called the microbiome – could also be a risk factor for allergies, asthma and diabetes.

“Over time, the scientific community has to create a more narrow spectrum of antibiotics to kill specific organisms and not all bacteria,” Blaser told ABCNews.com. “But we don’t have those yet.”

On average, American children receive 10 to 20 courses of antibiotics before their 18th birthday.

In 2008, the National Institutes of Health poured $115 million into the Human Microbiome Project – a “logical conceptual and experimental extension of the Human Genome Project,” according to a 2007 report in Nature.

“The [Human Microbiome Project] will address some of the most inspiring, vexing and fundamental scientific questions today,” the report authors wrote. “It is hoped that [it] will not only identify new ways to determine health and predisposition to diseases but also define the parameters needed to design, implement and monitor strategies for intentionally manipulating the human microbiota, to optimize its performance in the context of an individual’s physiology.”

The project could help guide treatments for various diseases, including obesity, just as the human genome has personalized some cancer therapies.

In September, German biochemist Peer Bork launched My.Microbes — a social network that promises to connect users with similar microbiomes to share digestive woes and diet tips. Joining will help researchers explore the link between gut bacteria and various ailments, but it will cost you $2,100 and some poop.