How Babies Born By C-Section Make Up for Lost Microbes

After nine months spent as a growing life in someone else’s body, the second a baby is born, they begin growing life in their own body: colonies of tiny bacterial cells ready to begin populating a baby’s gut microbiome. This microbial starter pack is a sort of going-away present from the mother’s body, acquired by a baby on the journey from the uterus through the birth canal. As a baby grows, their internal ecosystem becomes more complex, until eventually they’ve developed the robust bacterial diversity that allows the gut and other microbial havens to regulate and protect immunity and so many other elements of health.

This method of microbial transfer is a great evolutionary game plan. But in the modern world, there’s an issue: Not all babies take the same route out. Do infants born via C-section receive the same bacterial boon as those born vaginally?

The answer is no, and the question of how to remedy this deficit is at the heart of an emerging field of research. It’s also a question of increasing importance as the rate of C-section deliveries continues to rise in the U.S. By missing the vaginal canal, babies born by C-section have less microbial exposure at birth, but a paper published Mar. 8 in the journal Cell Host & Microbe suggests that there may be ways to compensate for this loss during the first few weeks of life.

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There’s no question that vaginal births impart more beneficial bacteria than C-sections, says Dr. Wouter de Steenhuijsen Piters, a physician and data scientist at the University Medical Center Utrecht in the Netherlands and senior author on the study. “When you compare emergency C-sections—when a woman has already gone into labor and the child has already passed into the birth canal partly—and elective C-sections, children [in the first category] are more similar to vaginally newborn children,” he explains. Past studies have looked at methods of compensating for missed microbial exposure, the most notable of which involves a practice called vaginal seeding, in which a mothers’ vaginal and sometimes fecal excretions are transferred to a C-section infant’s mouth or skin shortly after birth. These tactics have proved helpful for the infant microbiome, but some experts have expressed concern about associated risks, such as the unwanted transfer of harmful bacteria or viruses, including STIs. Ultimately, says Dr. Debby Bogaert, a pediatrics researcher at the University of Edinburgh and lead author on the study, this practice often just isn’t enough to fully fill the gap.

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The potential consequences of not receiving enough bacterial exposure at birth are fairly well understood. “For a long time, Cesarean section birth itself has been associated with certain outcomes—for example, obesity, Type-1 diabetes, and allergies,” explains de Steenhuijsen Piters. And the link is more than just associative, he adds. Specific microbial differences in C-section babies have been shown to directly cause some of these health conditions.

But despite any differences, says Bogaert, the simple fact that babies born by C-section live and grow shows that “any child is colonized. And the question was, where were these bacteria eventually coming from? And do they come from the mother from other sources or from the environment?”

In their new study, Bogaert and de Steenhuijsen Piters found that when babies born by C-section are breastfed, the microbes they receive from breast milk seem to compensate for the lack of microbes from other initial sources. “This was just entirely unknown,” Bogaert says. “It wasn’t until recent years that we could do these studies. We didn’t know, and we hadn’t considered it.”

Bogaert and de Steenhuijsen Piters’s research followed 120 Dutch mothers and babies, collecting skin, nose, saliva, and gut microbiome samples from the infants at two hours, one day, one week, two weeks, and one month post-birth. At each stage, they compared the unique microbiota they found to that of six different microbial hotspots on the infants’ mothers: their skin, breast milk, nose, throat, vagina, and feces. “We said, ‘Let’s try to put it all in one, holistic context—whole mom and whole baby,’” says Bogaert.

In all infants, regardless of delivery method, an average of 58.5% of their microbial landscape could be traced directly back to their mothers—a number they say reiterates the importance of things like skin-to-skin contact (including kisses and cuddles) in an infant’s first weeks. Even more interesting was their discovery that how the babies were delivered seemed to influence where on their mom the bulk of their bacterial colonies originated from. In analyses of babies’ feces two weeks post-birth, the percentage of the infant microbiome that could be traced back to maternal fecal contributions was two times larger in vaginally delivered babies than in babies delivered by C-section. Those same C-section babies, however, were found to have received nearly a third of their microbiome from breastfeeding, while the bacterial breakdown of vaginally born infants included only 11.2% that was traceable to breast milk. While some specific bacteria may still be missing, there’s also a remarkable amount of overlap across different areas of the body—meaning that breastfeeding is doing a lot of compensatory work to build up a baby’s systems. The authors also found that babies born via C-section who exclusively drink formula lack the rich microbiome that other C-section babies build up through breastmilk.

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“Everything that the baby gets from the mother seems important,” says Bogaert. Breastfeeding even transmits microbes not just from the milk, but from the skin contact as well. Bogaert says that she’d advise new mothers to hold and kiss their babies a lot, and to “really try and invest in the breast milk, even if it doesn’t work for the first days. If you can even attempt to breastfeed a little bit, all these microbes might matter a lot for your baby.” She says she’d also love to see fellow pediatricians being more judicious about when they give newborns antibiotics, as the drugs can disrupt their microbiota.

Bogaert and her colleagues acknowledge that when it comes to newborns, there’s often a fine line between encouraging empirical best practices and shaming new mothers for their choices—and what’s simply realistic, given that breastfeeding is time intensive and requires workplace support, which is often insufficient. “I really, truly believe that knowledge is power,” she says. “I have two teenagers. When they were born, we did not have this knowledge. And I wish we had, because it might have helped me and other mothers and fathers to make certain decisions.”

Maria Gloria Dominguez-Bello, a Rutgers professor who also studies early life microbiota and was not involved in the study, hopes that research like this will help prompt larger-scale societal changes that she believes are necessary to reduce the numbers of elective C-sections. She compares giving birth to running a marathon, but with a key difference: runners “have so much support. They have a backup team that is providing water, massaging their legs.” In contrast, in many communities that Dominguez-Bello has worked with, “the mothers are alone giving birth,” she says. “Every woman has the right to have a team supporting her during birth.” When she sees competent teams like this in action, she says, “you hear women say, ‘I had a fabulous experience giving birth.’ Society needs to provide a structure that helps the mothers and the babies.”

The experts agree that more research is needed to improve the birth experience and the essential days of early life, no matter how a baby is born. For Bogaert and de Steenhuijsen Piters, that means analyzing the rest of the data they collected from tracking their cohort through infancy and into childhood, in order to better understand the impacts of specific microbial differences. They also hope to break down more detailed information about where the other 40% of an infant’s microbiome comes from, looking at factors like dads, siblings, hospital environments, pets, and more.

But for now, one takeaway from their research that all new and expecting parents can put to good use, they say, is to really get in there and cuddle your newborn.