Of course, while farm animals often eat a significant dose of antibiotics in food, the situation is different for human beings. By the time most meat reaches our table, it contains little or no antibiotics. So we receive our greatest exposure in the pills we take, rather than the food we eat. American kids are prescribed on average about one course of antibiotics every year, often for ear and chest infections. Could these intermittent high doses affect our metabolism?

To find out, Dr. Blaser and his colleagues have spent years studying the effects of antibiotics on the growth of baby mice. In one experiment, his lab raised mice on both high-calorie food and antibiotics. “As we all know, our children’s diets have gotten a lot richer in recent decades,” he writes in a book, “Missing Microbes,” due out in April. At the same time, American children often are prescribed antibiotics. What happens when chocolate doughnuts mix with penicillin?

The results of the study were dramatic, particularly in female mice: They gained about twice as much body fat as the control-group mice who ate the same food. “For the female mice, the antibiotic exposure was the switch that converted more of those extra calories in the diet to fat, while the males grew more in terms of both muscle and fat,” Dr. Blaser writes. “The observations are consistent with the idea that the modern high-calorie diet alone is insufficient to explain the obesity epidemic and that antibiotics could be contributing.”

The Blaser lab also investigates whether antibiotics may be changing the animals’ microbiome — the trillions of bacteria that live inside their guts. These bacteria seem to play a role in all sorts of immune responses, and, crucially, in digesting food, making nutrients and maintaining a healthy weight. And antibiotics can kill them off: One recent study found that taking the antibiotic ciprofloxacin decimated entire populations of certain bugs in some patients’ digestive tracts — bacteria they might have been born with.

Until recently, scientists simply had no way to identify and sort these trillions of bacteria. But thanks to a new technique called high-throughput sequencing, we can now examine bacterial populations inside people. According to Ilseung Cho, a gastroenterologist who works with the Blaser lab, researchers are learning so much about the gut bugs that it is sometimes difficult to make sense of the blizzard of revelations. “Interpreting the volume of data being generated is as much a challenge as the scientific questions we are interested in asking,” he said.

Investigators are beginning to piece together a story about how gut bacteria shapes each life, beginning at birth, when infants are anointed with populations from their mothers’ microbiomes. Babies who are born by cesarean and never make that trip through the birth canal apparently never receive some key bugs from their mothers — possibly including those that help to maintain a healthy body weight. Children born by C-section are more likely to be obese in later life.

By the time we reach adulthood, we have developed our own distinct menagerie of bacteria. In fact, it doesn’t always make sense to speak of us and them. You are the condo that your bugs helped to build and design. The bugs redecorate you every day. They turn the thermostat up and down, and bang on your pipes.