06.02.134:45 AM ET

My Baby, My Microbiome

Evidence is mounting that babies delivered by C-section miss out on the benefits of the mother's microbiome. Karen Levy on how cesarean's could be tied to obesity, asthma, allergies and more.

In January I gave birth to my second child. At the end of my pregnancy I was told that my daughter was in a breech position, making delivery by cesarean section highly likely. I was thankful for the option of a safe delivery of my breech baby, but I was also worried.

Like many women, I wondered how my scar would look in a bikini and how I would take care of an infant while recovering from major surgery. But as a microbiologist, these were not my primary concerns. Instead, my first thought was of my vaginal microbiome. I wanted my baby to have access to it. Michael Pollan recently provided an excellent overview about the burgeoning field of human microbiome research in his cover story for The New York Times Magazine. He aptly describes the latest research on the trillions of bacteria and other microorganisms that live in our gut, on our skin, and in other parts of our bodies.

Some of the microbes that take up residence in our bodies can cause harm, but the vast majority are helpful and even necessary for bodily functions. Think of the human body as an office building, with a physical structure and all of the necessary electrical and plumbing systems. The building needs desks, filing cabinets and computers to make it a productive system, just like the thousands of species of microorganisms that we support make us a functioning system. For example, the microbes in the gut determine how efficiently a person processes nutrients, and help to regulate our metabolism.

As an expectant mother, I had been paying especially close attention to studies about how pregnancy and labor can affect the establishment of the infant gut microbiome, and how the composition of the gut microbiome can impact a baby’s health. In the womb, an infant’s gut is sterile, but it is colonized with bacteria immediately following birth. Most babies acquire their mother’s bacteria in the vaginal canal on their way into the world. Researchers have shown that if a baby is born vaginally, its bacterial community resembles that of the mother’s vagina. If a baby is born by C-section, its bacterial community resembles that of the mother’s skin.

Why does this matter? Because the microbes passed from a mother’s vagina to an infant’s gut can help an infant face the many challenges of his or her new environment. For example, during pregnancy, the composition of bacteria in a woman’s vagina changes so that there is a higher concentration of Lactobacillus, a kind of bacteria that aids in the digestion of milk. While he or she might eventually get colonized, a baby born by cesarean section will miss out on immediately acquiring these beneficial bacteria. And mode of delivery has been associated with differences in intestinal microbes even seven years after delivery.

Gut colonization by microbes is delayed in C-sectioned babies, which may explain in part why these infants have a harder time fighting off infections. Immediately after birth, the establishment of gut bacteria can affect the development of the immune system. A baby’s gut microbiota can also affect its disposition in the first weeks and months of life. Dutch researchers recently published a study in the journal Pediatrics showing that infants with colic have more bacteria that are known to produce gas, whereas anti-inflammatory bacteria that live in the vaginal canal are more common in colic-free infants.

Scientists are starting to draw connections between the gut bacteria in infants and an increasing number of health problems that are more common in children born by C-section, such as obesity, asthma, allergies, type 1 diabetes, food allergies, eczema, and celiac disease. While there is still much we don’t know, alterations to the gut microbiome might connect these conditions to what some have dubbed the "cesarean epidemic" in our country and around the globe. Today one of every three infants born in the United States is delivered by cesearean section. The high rate of C-sections may be affecting our collective microbiome. This is an issue for thousands of women and their babies—one they are almost entirely unaware of.

While C-sections can be medically necessary, many can be avoided. The role of obstetricians is to bring healthy babies into the world, but perhaps we should reconsider what constitutes a “healthy” and “safe” delivery. The new research on infant gut colonization by microbes should lead us to address not only the moment of birth but also longer-term health outcomes.

Short of reducing the caeserean delivery rate, we should also apply the advances in our understanding of the microbiome toward therapies that help cultivate beneficial bacteria in infants. For example, giving infants probiotics (“good” bacteria) has been shown to successfully reduce both colic and eczema. But it is hard to know how to choose which bacteria to use. Rather than trying to engineer a particular mix of microbes, one idea would be to inoculate babies born by cesarean section with their mothers’ vaginal fluids, either by application to the baby’s skin or putting a little bit of fluid into their mouths. In his article, Pollan reports that other scientists have done this and a formal trial of the procedure is underway in Puerto Rico.

Babies born vaginally are naturally inoculated during birth. Babies born via C-section could receive the same benefits with this simple procedure, mimicking the process of a natural passage into the world. After reading a great deal of scientific literature in the days leading up to my own delivery, I became increasingly convinced that I didn’t want to wait for the results of a clinical trial. I wanted my baby to receive the microbial community that Mother Nature had provided me as a mother. In the end, my daughter flipped and I delivered her vaginally. But if she hadn’t, I would have taken things into my own hands, quite literally, and inoculated her myself shortly after birth by putting some of my vaginal fluid into her mouth.

And then I would have started to worry about my bikini line.

Karen Levy is an assistant professor of environmental health at Emory University and a Public Voices Fellow with The Op-Ed Project.