Baby health

Why your baby's gut bacteria is so important

The trillions of good bacteria in our intestines are key to protecting us from infection and illness. Since babies are born with a gut bacteria count of zero, it's crucial to build it up in the first few months and years. Here's how to do it and why it really matters.

Why your baby's gut bacteria is so important

Photo: Stocksy United & Tony Lanz

Holly WhiteKnight was in labour last December when her baby boy, Frederick, flipped in her uterus, settling head up. The Kingston, Ont., naturopath had been planning on a vaginal birth for its many benefits—including all the good bacteria Frederick would collect on his way through her birth canal—but didn’t want to risk trying one, given that her baby was now breech. So when WhiteKnight’s doula quickly explained vaginal seeding, an alternate way for a mother to pass her healthy vaginal flora on to her newborn for good baby gut health, there was no time to waste.

With her C-section an hour away, WhiteKnight got the go-ahead from her medical team at Kingston General Hospital. The obstetrician on call inserted a piece of saline-soaked sterile gauze into her vagina and left it there until just before the surgery, when it was removed and held in a sterile container. “When they got Frederick out, a nurse immediately put the cultured gauze in his mouth, in his nose, and over his eyes and face, and then wiped the rest of his body down,” says WhiteKnight. “For me, it was so empowering. I just wanted to give him the best start possible.”

While vaginal seeding is not yet widely practised, it’s big news among scientists who study the gut—a field of research that’s growing rapidly. In a small study currently under review, Maria Gloria Dominguez-Bello, a microbiologist at New York University School of Medicine, showed that the technique—swabbing babies post C-section with their mother’s vaginal bacteria—helps make a newborn’s intestinal bacteria more diverse. A healthy population of microbes is, in this case, a very good thing for baby gut health—though it’s an adjustment in thinking, particularly for germ-wary new parents.

Graeme Smith, head of obstetrics and gynaecology at Queen’s University and Kingston General Hospital, and WhiteKnight’s OB, is keen to better understand how contact with mom’s bacteria affects the development of an infant’s own bacterial community—and how beneficial it is to baby’s health. He’s eager for the next phase of Dominguez-Bello’s study: a larger group of swabbed C-section babies, which she will observe for three years to determine whether those bacteria that manage to wiggle their way to the infants’ guts—as Smith puts it—have any positive, tangible impact.

“As funny as it sounds, that’s what happens when a baby is born vaginally,” Smith says. That bacteria-laden passage—or post-surgery swab—is baby’s first contact with the microbes that cover us, live inside us and are important for our health because, as Smith says, “babies are essentially born sterile.” However, he adds that very early research now suggests there may be some microbes present in the placenta, which means early seeding might even start before delivery.

Adults are a different story: We house trillions of microbes (more helpful than harmful) in our intestines. These bacteria—otherwise known as our intestinal microbiota—play a significant role in our overall health. They help with digestion and train our immune system to recognize invaders, protecting us from sickness and disease. Our intestinal microbiome is so complex and important that researchers have begun to think of it as a virtual organ—one that develops significantly in the first few months of life.

“As soon as a baby emerges from the amniotic sac, the theory is that his gut begins to accumulate the bacteria that are going to populate it and influence its immune system,” says Smith, noting that most children’s microbiomes are well-established by age one and fully developed by age three. For babies born vaginally, the birth canal is their first exposure. For babies delivered by C-section, initial contact is with a surgeon’s sterile gloved hands, but soon after (ideally), mom’s chest, when they are placed skin to skin. Naturally, breastfeeding is an extension of this—Smith says the breast appears to be the most important source for establishing a diverse microbiome in newborns.


“A lot of a baby’s microbiome is built from skin-to-skin contact with mom [in],” Smith says, pointing out that some bacteria make their way inside our bodies to our intestines, while others live on our skin, under our fingernails, in our noses and on our genitals. “My hospital does early skin-to-skin contact for this reason, and that should be promoted at every hospital, along with breastfeeding and vaginal delivery, when possible.”

One of the most interesting findings to emerge from the buzz around bacteria and baby gut health: the potential protection that good gut bacteria may ensure against hay fever, asthma and eczema—an interconnected trio known as atopic diseases. A study published last spring in the journal Clinical and Experimental Allergy, co-authored by Anita Kozyrskyj, a researcher in molecular epidemiology at the University of Alberta, showed that infants with fewer different strains of bacteria in their intestines at three months (determined by analyzing stool samples) had an increased risk of developing a reaction to foods like milk, eggs and peanuts by one year of age (verified via skin-prick allergy testing). Some of those infants were then also more likely to develop atopic diseases.

A University of British Columbia study published this fall went one step further. Co-authored by Brett Finlay, a professor of microbiology and immunology, the study looked at 319 one-year-olds who were likely to develop asthma because they wheezed and tested positive for allergens on a skin-prick test. Researchers had been following these kids from birth as part of a Canadian survey of almost 3,500 children.

Finlay and his team analyzed the stool samples of three-month-old babies who had gone on to develop asthma by their first birthday. They found they were missing or had low levels of four key bacteria—bacteria that were present in one-year-olds without asthma. What’s more, when those four bacteria were injected into sterile, germ-free mice, they showed “markedly fewer asthma symptoms, including lung inflammation,” he says.

Since using young mice is a reliable way to mimic what might happen in young humans, the results open the doors for more breakthroughs, Finlay says. “The exciting thing is this: Could we identify high-risk kids? And if they’re at risk [for], could we then add a probiotic-like cocktail of these four microbial species [to] to see if we can influence the outcome?” Down the road, this could be used as a way to prevent asthma, identifying and treating at-risk babies within the first few months of life to bolster their microbiomes. “That’s where we’re headed with it.”


Smith hopes that more research into vaginal seeding will prove this theory: that babies swabbed immediately post-C-section will be less likely to develop asthma, eczema or hay fever than those babies who aren’t, eventually making the practice more standard than experimental.

Beyond delivery and breastfeeding, possibly one of the easiest ways to ensure good baby gut health: Don’t stress about housekeeping.

According to a Johns Hopkins Children’s Center study published last year in the Journal of Allergy and Clinical Immunology, infants exposed to a wide variety of household bacteria and animal dander in the first year of life appear to be less likely to suffer from food allergies and asthma than those who live in spotless homes.

For Finlay, the key to healthier kids might be simply to “let kids be kids”—sampling crumbs off the ground and licking shopping cart handles as they please seems to improve gut health. “We need to rethink how we behave as a society,” he says. “We’ve gone hyper sterile, with the idea of getting rid of every microbe. But I think we’re seeing the consequences now, with more kids with allergies, asthma and eczema than ever before.”

Ask your caregiver Graeme Smith, head of obstetrics and gynaecology at Queen’s University and Kingston General Hospital, doesn’t recommend women and their delivery teams try vaginal seeding on their own. Along with the transfer of good bacteria, it might inadvertently pass along harmful bacteria, such as group B streptococcus and bacteria that cause gonorrhea or chlamydia—strains you might not be screened for when a C-section is planned.


A version of this article appeared in our December 2015 issue with the headline, “Gut feeling”, p. 28.

This article was originally published on Nov 08, 2016

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