The human gut teems with bacteria. There are 10 microbes in the body for every human cell thanks mainly to the profusion of colonies in the intestines. Yet babies are born without any such germ populations; rather they develop them in fits and starts over time. Now researchers have mapped this development for the first time in 14 California babies, including a set of fraternal twins.

Researchers collected an average of 26 stool samples from each baby from their very first bowel movement to subsequent ones, including those following major events such as travel, illness or treatment with an antibiotic. Geneticist Chana Palmer, now a program director at the Canary Foundation in San Jose, Calif., which focuses on early cancer detection, and colleagues at Stanford University then tested each sample to glean what microbes lurked within. Palmer used a new tool—a microarray designed to detect differences in the ribosomal RNA of different microbes—to assess the whole panoply of microscopic critters inhabiting the babies' guts.

"The infant's gut is an exciting and rapidly evolving place," Palmer says. "Populations are quite unstable over the first few months but by a year of age they resemble each other and also resemble adult guts." Among the microbes that eventually dominate: Bacteroides, Eubacteriales, Clostridium, Ruminococcus and Faecalibacterium, as well as small amounts of fungi and archaea.

But these microbes did not start out at the top of the bottom. In fact, infants are born with no bacterial colonies at all but they subsequently develop a wide variety in their guts—and how long that process takes. "Some were in 24 hours," Palmer notes. "The twins were both the latest," taking a full week to develop comparable numbers of bacteria.

She speculates that the single set of fraternal twins in the study may have developed colonies slowly because they were the only subjects delivered by planned caesarean section, meaning there was no contact with their mother's microbial community. But the twins also demonstrated that genetics plays a role in determining the gut's microbial makeup; their intestinal flora were more similar to one another's than to those of any other baby, and even more so than to the intestines of parents or siblings and related infants, Palmer says.

The research results, published this week in PLoS Biology, indicate that all babies seem to acquire the same set of bacteria over time, though they start in radically different places and experience dramatically different shifts in the populations over the first year. Future experiments with the ribosomal RNA microarray will compare healthy and sick infants and the effects of antibiotics on adult gut populations. The Human Gut Microbiome Initiative is seeking to sequence all this genetic material. Yet, it remains unclear what kind of microbes are best for your—or your baby's—gut. "We really have no idea," Palmer admits, "what is ideal."