Does Having a C-Section Alter Baby’s First Microbiome?

A study of cesarean babies swabbed with birth canal fluids suggests that some newborns may be missing out on helpful microbes

Mom and baby share a lot, including their microbial ecosystems. Halfpoint/iStock

William Wordsworth was on to something. As the poet claimed, a newborn never enters the world in utter nakedness but instead comes trailing clouds of glory—if by clouds of glory you mean a coating of mostly helpful microbes picked up from the fluids inside mom's birth canal.

But studies suggest that babies born via cesarean section, or C-section, miss out on exposure to many of these beneficial microbes, which may have an impact on their long-term health. Disruption to the infant microbiome from modern practices like antibiotics use, bottle feeding and elective C-section births has been associated with conditions such as asthma, allergies, type 1 diabetes and obesity.

Now Maria Dominguez-Bello, of the New York University Langone Medical Center, and her colleagues may have a way to restore at least part of that lost microbiome and better mimic the microbial mix that natural-birth babies acquire—a bath in mom's vaginal fluid.

The unusual technique does appear to add diversity to the infant microbiome, according to a study published today in Nature Medicine. But it's not yet clear what, if any, impact it could have on the future health of C-section infants.

C-section deliveries can save the lives of both babies and moms. The World Health Organization (WHO) suggests that some 10 to 15 percent of all births worldwide involve a medically necessary C-section, and in some countries people who lack access to these procedures suffer unnecessary loss of life.

But women can also chose to have a C-section, for reasons that vary across countries and cultures. These births may be considered safer, pain-free, convenient and perhaps less traumatic for the newborn—though medical studies don't support these benefits beyond the 10 percent level of people who need C-sections for medical reasons.

Still, elective C-section rates are rising in many developed nations. In the U.S., about 30 percent of all births are by medical or elective C-section. Other countries have far higher rates. In Brazil, for instance, the number can top 80 percent in private hospitals and over 50 percent in the public health care system. 

One worry is that all those C-section babies are missing out on exposure to invisible, and possibly important, microbes. Previous studies showed that babies born vaginally have microbiomes that resemble the bacterial communities of their mom's vagina, while C-section babies do not.

Dominguez-Bello and colleagues developed an intriguing way to alter that equation. They placed sterile gauze inside the vaginas of mothers for an hour before their C-sections, then swabbed their babies' bodies and mouths with the gauze just after birth to simulate the early exposure to microbes that the infants would have experienced in the birth canal.

During the first month of life, those babies' microbiomes, particularly those of oral and skin bacteria, looked more like those of babies born vaginally—both had higher concentrations of Lactobacillus and Bacteroides, species that help infants' immune systems recognize and not fight off helpful bacteria. These beneficial groups weren't found at nearly the same levels in conventional C-section babies.

“Our study shows significant differences in the bacterial communities of C-section infants exposed to their maternal vaginal fluids, whose microbiota is partially restored and more similar to that of vaginally delivered infants,” study co-author Jose Clemente, of the Icahn School of Medicine at Mount Sinai, said during a press conference last week. However, the study was only a very small pilot. The scientists swabbed 4 babies out of 11 C-section deliveries, and compared them to 7 vaginal births.  

Alexander Khoruts, a gastroenterologist at the University of Minnesota, adds that while the study was intriguing, the underlying reasons that people have C-sections may also be playing a role in infants' long-term health.

“Many [C-sections] are done for medical reasons, so right away you're starting with a difference from the scheduled C-sections in this study," he says. "So there's a part of me that wants to say hold on, we don't know what the problem is yet. But it certainly does make sense. It's logically compelling to think that this inoculation, the passage in the birthing process, would have an effect on the microbiome.”

Another caveat concerns which of the body's many bacterial communities are being affected. Previous work suggested that the biggest differences in the early microbiomes of C-section versus vaginal birth infants is in their acquisition of gut microbes.

“Ninety-nine percent of the microbes you'd expect to be in the gut, because that's where the food is,” Khoruts notes. “So if we look at what was changed in the study in terms of biomass, the gut microbes have changed little with this intervention. They look much more like a C-section baby's than a vaginal birth baby's.”

Sharon Meropol, a pediatrician at Case Western Reserve University School of Medicine and Rainbow Babies & Children's Hospital, recently authored an Embryo Today review on development of the infant microbiome. She calls the new study interesting and well-done, but like the authors themselves, she notes that the research was further complicated by the infants' differing exposure to antibiotics.

Moms routinely receive antibiotics during pregnancy or labor to ward off infections. C-section mothers are usually given antibiotics, and all seven of the study's C-section mothers received them at some point before birth, while only about half of the vaginal delivery moms did.

“Antibiotics of course decrease bacterial diversity and select for certain species over others, and infants can be exposed to maternal antibiotics through the placenta,” Meropol says. “This is a bit confusing and makes comparison a bit difficult.”

What's more, figuring out successful ways to alter the infant microbiome won't matter much unless scientists can be certain that such interventions actually help human health.

“We would like to emphasize that our study establishes feasibility but not any health outcomes,” Clemente cautioned. Much more research will be needed to see if the process might be “translated into reducing the disease risks associated with C-section births,” he says.

That makes the new results an intriguing piece of a very complex puzzle that scientists are still striving to solve, Khoruts notes. 

“We have this huge question: Why are we having marked increases in diseases of autoimmunity?” he asks. “There's probably more than one answer, but is the infant microbiome part of the reason? If it is, it's probably the developmental period that's most important, so what are the most important factors that go into shaping that very early microbiome? One of them may well be this issue of vaginal birth versus C-section.” 

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