Baby's Beneficial Bacteria Depend on Birth

By Rachel Ehrenberg for Science News
posted with permission

Water to water: baby enters the world vaginally into warm waters and his mother's waiting arms. Photograph by Sandi Heinrich. Property of Natural Blessings Doula Services, used with permission.

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 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, published 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 rare cases when truly needed, 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 per day, which may harbor some of the mother’s microbes, Neu speculates.



Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

Study Authors:

Maria G. Dominguez-Belloa
Elizabeth K. Costellob
Monica Contrerasc
Magda Magrisd
Glida Hidalgod
Noah Fierere
Rob Knight


Upon delivery, the neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes the microbiota's establishment and, subsequently, its role in child health, most researchers have focused on specific bacterial taxa or on a single body habitat, the gut. Thus, the initiation stage of human microbiome development remains obscure. The goal of the present study was to obtain a community-wide perspective on the influence of delivery mode and body habitat on the neonate's first microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities from mothers and their newborn babies, four born vaginally and six born via Cesarean section. Mothers’ skin, oral mucosa, and vagina were sampled 1 h before delivery, and neonates’ skin, oral mucosa, and nasopharyngeal aspirate were sampled <5 min, and meconium <24 h, after delivery. We found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode. Our results also show that vaginally delivered infants acquired bacterial communities resembling their own mother's vaginal microbiota, dominated by Lactobacillus, Prevotella, or Sneathia spp., and C-section infants harbored bacterial communities similar to those found on the skin surface, dominated by Staphylococcus, Corynebacterium, and Propionibacterium spp. These findings establish an important baseline for studies tracking the human microbiome's successional development in different body habitats following different delivery modes, and their associated effects on infant health.

To view Full Text of this study, visit the Proceedings of the National Academy of Sciences of the United States of America.


  1. This has been on my mind a lot lately. I had a vaginal birth but I had to have antibiotics during labour for Group B Strep. No one explained the side effects to me and I didn't find out about how the baby's colonization occurs until months after. My son has a lot of food sensitivities and I wonder if the two are related.

  2. Our bodies work the way they do for good reasons. Science is barely scratching the surface of how it all fits together--otherwise our organs (uterus, tonsils, appendix, gallbladder, etc.) wouldn't be considered unnecessary.

    While I feel it is good we continue to find more information on how birth works I worry that it is just in an effort to attempt a scientific recreation--kind of like trying to make formula better by researching the wonders of breast milk rather than supporting breast feeding itself.

  3. This is a great article. I'm super glad I'm breastfeeding my c-section born baby, to give her the best possible start, given her circumstances! All is not lost :)!

  4. By the time we have our next 2 babies I will have had 6 c-sections



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