Researchers delve into diapers to discover what types of bacteria establish a home in the human gut.

Scientists have found that the mix of bacteria in a baby's gut is shaped over time.

A baby may get her eyes from mom and her hair from dad, but where does the bacteria in her gut come from? To answer this question, HHMI investigator Patrick O. Brown at Stanford University School of Medicine and colleagues found themselves up to their ears in diapers—about a year's worth—to analyze the microbial contents of newborns' bowels.

Babies are born with a sterile intestinal tract, but within a matter of days bacterial colonies establish themselves in the gut, eventually (by adulthood) outnumbering human cells 10 to 1. These multiplying microbes serve numerous purposes, including protecting against harmful pathogens and aiding digestion.

"The tricky thing is that we don't really know what the ideal population looks like," says Chana Palmer, Brown's former graduate student and first author of their July 2007 PLoS Biology report.

To get a view of the bacteria found in the gut, Palmer collected stool samples from 14 babies and their parents at several intervals over each baby's first year (see "Baby Biology," Centrifuge). She spread fluorescently labeled DNA from the samples on a microarray glass chip dotted with known bacterial DNA. Samples whose DNA sequence matched any bacterial sequence on the chip latched onto those spots and were tallied by a computer.

Hundreds of different species of bacteria were found to inhabit an infant's gastrointestinal tract, and each baby had a different mix. The fraternal twins in the study showed the most similarity, suggesting that genetics and environment work together to shape the gut population in a reproducible way. By year one, all the infants had a generalized profile close to that of an adult.

"It almost doesn't matter where you start off because we all end up in the same place," says Palmer. "There are some bacteria that are really well suited for your gut and they're going to win no matter what."

Whether bacterial flora are a function of genetics or the environment or both remains to be tested, says Brown, who likens the process to gardening. "What comes up depends both on what seeds were sown and which are best suited to the particular soil and climate."

Photo: Visuals Unlimited / Corbis