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Birth of an Intestinal Ecosystem

Eating dinner alone tonight? Think again. You may be the only person at the table, but inside your gut are a hundred trillion or so single-celled organisms, collectively called microbiota. Some of the services provided by these friendly bacteria—such as helping you process your food and protecting you from unfriendly germs—are known to scientists, at least in rough terms. But, for the most part, your gut ecosystem is unexplored territory. How many different species of bacteria live there? What roles, exactly, do they play in health and disease? How does the make-up of the gut microbial ecosystem differ from person to person?

Snapshots of a New Gut-level World

To find out the answers, David Relman, M.D., of Stanford University, and his colleagues started at the bottom—specifically, the bottoms of babies. At birth, the gut is completely sterile. But within days, the first microbial denizens take up residence. The researchers enlisted parents of 14 infants (including one set of twins) to collect stool samples from their babies on a defined schedule over the course of a year, beginning with baby’s first bowel movement. Stool samples provide a non-invasive way for the researchers to gauge how each infant’s gut microbiota assembles and develops. The investigators extracted genetic material from the samples and used DNA microarray technology to take a series of snapshots of each infant’s microbial community. Microarrays are glass wafers dotted with many thousands of DNA spots of known genetic sequence. For this study, the Stanford scientists designed a novel microarray that included a little-varying bacterial gene that can recognize thousands of distinct microbial species.

Newborn to Nearly Grown in Just One Year

A total of 363 infant stool samples were analyzed and compared with a smaller number of stool, vaginal fluid, and breast milk samples taken from some of the babies’ family members. The babies varied widely in the composition of their intestinal microbiota, at least for the earliest part of their lives, the scientists determined. “Certain bacteria appeared and then suddenly dropped in abundance, and other bacteria appeared and took their place,” said Dr. Relman. The early colonizers included species able to survive in oxygen-containing environments, such as staphylococcal and streptococcal bacteria, while later-appearing species were types predicted to prefer or require oxygen-free environments. By a baby’s first birthday, however, the composition of the intestinal microbiota had stabilized and become more like the gut ecosystem seen in adults. In adults, as in the one-year-olds, more than 99 percent of all gut microbiota fell into just 3 (out of 22 possible) broad microbial groups.

The twins were delivered by cesarean section—and thus were not exposed to their mother’s vaginal microbiota. Those infants, the researchers found, had lower total bacterial counts in their guts during the first week of life, but quickly caught up to the other infants. Unlike the other 12 babies, each with a unique microbiota composition profile, the twins shared a strikingly similar pattern of bacterial abundance throughout the year. Six of the babies took antimicrobial medicine during their first year of life; in one case in particular, the researchers saw a dramatic impact of antibiotics on the intestinal microbiota.

This first foray into the birth of an ecosystem has established a foundation for future explorations, notes Dr. Relman. For example, all of the babies in this study were full-term and breast-fed, yet their intestinal microbiota showed a surprising degree of variation in the early weeks and months. Future research may investigate what effect premature birth or formula feeding plays in the establishment or composition of the gut microbiota.


Palmer C et al. Development of the human intestinal microbiota. PloS Biology 2(7) e177 DOI: 10.1371/journal.pbio.0050177 (2007).

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Last Updated February 18, 2009