By Rachel Ehrenberg, Science News

It’s the journey, not the destination,that determines the quality of bacteria a newborn encounters in life’s first moments.

A new survey finds that babies born via cesarean section had markedly different bacteria on their skin, noses mouths and rectums than babies born vaginally. The research adds to evidence that babies born via C-section may miss out on beneficial bacteria passed on by their mothers.

“We know from lots and lots of other ecosystems that how you set up the house has a real impact for all the later guests,” says medical microbiologist David Relman of the Stanford University School of Medicine, who was not involved in the study.

Previous research suggests that babies born via C-section are more likely to develop allergies, asthma and other immune system–related troubles than are babies born the traditional way. The new study, to be published online the week of June 21 in the Proceedings of the National Academy of Sciences, offers a detailed look at the early stages of the body’s colonization by microbes, critters that shape the developing immune system, help extract nutrients from food and keep harmful microbes at bay.

Babies born vaginally were colonized predominantly by Lactobacillus, microbes that aid in milk digestion, the research team from the University of Puerto Rico, the University of Colorado in Boulder and two Venezuelan institutes report. The C-section babies were colonized by a mixture of potentially nasty bacteria typically found on the skin and in hospitals, such as Staphylococcus and Acinetobacter.

The new work may improve understanding of the early immune system, says Gary Huffnagle of the University of Michigan in Ann Arbor. While C-sections can be lifesaving in some cases, the procedure appears to shift a baby’s first bacterial community. A better understanding of this early colonization, which is also influenced by events such as breast-feeding, may lead to medical practices for establishing healthy bacterial colonization.

“This isn’t damning the C-section, but it may be important to make sure your child gets a mouthful of vaginal material,” says Huffnagle.

The study included nine women and their 10 newborns (including one set of twins) born at the Puerto Ayacucho Hospital in the state of Amazonas, Venezuela. The mothers’ skin, mouths and vaginas were sampled an hour before delivery. Babies’ mouths and skin were swabbed immediately after birth, and their rectums were swabbed after their first bowel movement. DNA analysis revealed that the four babies born vaginally carried bacterial populations that matched those of their mothers’ vaginas, while the C-section babies had a more generic mixture of skin bacteria, similar to that found on the skin of all the moms.

“The vaginal birth was like a fingerprint of mom,” says study coauthor María Domínguez-Bello of the University of Puerto Rico in San Juan.

First-comers to the body are critical for establishing the microbial scene, says pediatrician Josef Neu of the University of Florida in Gainesville. “It’s like a garden where few, if any, seeds have been planted. If you push in one direction you might get a lot of weeds, a lack of diversity,” Neu says. “That can be associated with immune system problems.”

Some work suggests colonization may begin even earlier. While the paradigm has been that babies are sterile until birth, Neu’s recent work found a microbial community already dwelling in the first poop of some babies born prematurely. While a baby is in the uterus, it typically swallows 400 to 500 milliliters of amniotic fluid, which may harbor some of the mother’s microbes, Neu speculates.

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