Baby Microbiome: Nurturing Your Baby's Healthy Bacteria

Medically Reviewed by Hansa D. Bhargava, MD on September 30, 2019
5 min read

By now, you've heard the news: The trillions of bacteria that inhabit your gut and other bodily regions can have a critical impact on your overall health. The same holds true for babies, new research shows.

"The microbiome is important for many aspects of health, from gut health to mental health to immune health, and we're finding that the first couple of months of life is a really critical window for its development," says Meghan Azad, a microbiome researcher and assistant professor of child health at the University of Manitoba.

Recent studies suggest that babies whose microbiome development is disrupted via a cesarean section delivery, early antibiotic use, limited breastfeeding, or other factors are at greater risk for a host of health conditions, including asthma and allergies, respiratory infections, irritable bowel disease, type 1 diabetes, and obesity. But they also suggest that no matter how a baby is delivered, parents can take steps to get baby's bacterial ecosystem off to a good start.

By the time people reach adulthood they host between 500 and 1,000 species of gut bacteria, many of them beneficial, which serve to fight off infection-causing microbes, digest food and metabolize nutrients, and interact with the central nervous system to influence mood and cognitive health. The foundation for that bacterial collection is established by age 3, and what happens in the first three months of life is key.

"Babies are born with essentially no microbiome and a very immature immune system, and the two develop together, informing each other," says Azad, noting that the first microbes to colonize a baby's gut, skin, and mouth help teach the immune system what's harmful and what's not. "When there are microbes missing, and that immune system doesn't develop properly, there can be a greater risk of developing problems."

Vaginal birth, when possible, marks a critical step, exposing an infant to a diverse array of mom's bacteria as he or she passes through the birth canal.

"Babies born via cesarean section don't get that same degree of exposure," says Sara Edwards, PhD, a certified nurse-midwife and microbiome researcher at Emory University School of Nursing.

In one recent study, researchers looked at stool samples of 120 infants 10 times over their first year of life and found that those born vaginally had more beneficial bacteria and fewer harmful bacteria. Another recent study of more than 6,000 infants born in New York found that those born via cesarean section were twice as likely to develop food allergies or asthma by age 3.

"Evidence from this and other studies suggests that the bacteria a mother passes to her baby during vaginal delivery may serve to protect the child from developing asthma and food allergies," the authors concluded.

Edwards notes that even if a mother labors for a little while after her water has broken, that exposes an infant to beneficial microbes. In general, infants born via emergency cesarean section (after some labor) have a healthier microbiome than those born via scheduled cesarean section.

While it's too early for doctors to recommend it, some researchers have begun to study whether a practice called "vaginal seeding" -- in which a cotton swab is used to inoculate a newborn's skin, nose, and mouth with fluids from the birth canal -- may be helpful for establishing a healthy microbiome in babies born via cesarean section.

In the meantime, in cases when a cesarean section is unavoidable, Edwards says lots of skin-to-skin contact between mom and baby immediately after birth can help inoculate a newborn with mom's good bacteria.

No matter how a baby is delivered, his or her first diet sets the stage for the microbiome.

"Breastfeeding is the most important way to support a baby's microbiome," says Azad, who recommends breastfeeding exclusively for six months whenever possible, then continued breastfeeding after the introduction of complementary food.

In addition to passing beneficial microbes from mom to baby, breast milk contains compounds called human milk oligosaccharides (HMOs) which serve as food for key beneficial bacteria, including Bifidobacterium and Bacteroides. Research shows that babies born via cesarean section catch up faster, in terms of microbiome development, if they are exclusively breastfed. And one recent study of 323 infants found that those who were exclusively breastfed had a healthier and more diverse microbiome at 6 months than those fed with formula.

"Companies are trying to make formula as close to human milk as possible, which is a good goal, but it will never be the same," says Azad. "Each mom's milk is different and personalized for her own baby."

Edwards also recommends that moms minimize their own use of antibiotics -- which can wipe out both good and bad bacteria -- while they are pregnant and breastfeeding and be equally prudent with antibiotic use for their new babies.

And she cautions against introducing solid foods before 6 months, as they can prematurely alter the gut microbiome before it's ready, boosting risk of stomach problems. "This is a critical time of life in which the brain and body are developing, but the gut is also developing," says Edwards. "By nurturing it, we can actively promote a baby's health in a way that has long-term consequences."


Percentage more likely babies born via cesarean section are to be obese by adolescence than their siblings born vaginally.


Amount more likely babies born via cesarean section to have allergies or asthma by age 3.


Percentage of all deliveries that are now via cesarean section.


Percentage of babies who are still breastfeeding at 6 months.


Number of years a baby's first diet can impact his or her microbiome.

Give your baby's biome a boost with a few pointers from Edwards.

1. Direct From Mom

Offer breastmilk straight from the source whenever possible. Studies show it provides more good bacteria and less harmful bacteria than pumped milk.

2. Moderation in Bathing

Don't overdo it on the baths, which can strip baby's skin of beneficial bacteria.

3. Pass it On

Eat bacteria-rich food like kimchi, kraut, yogurt, and kefir while you're pregnant and breastfeeding. The more beneficial microbes you have, the more you can pass to baby.

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