The Miracle of the Infant Microbiome

infant microbiome

Whether you’re anxiously awaiting the arrival of your bundle of joy or are already wrapping your newborn baby safely in your arms, you’re likely immersed in the wonder and beauty of all things baby—from their adorable fingers and toes to their perfect soft skin.

What you may not be thinking about as you daydream about the newest member of your family is the importance of their microbiome, the teeming colonies of bacteria starting to set up shop throughout their tiny body.

You see, each and every one of us has a miraculous microbiome that works to, among many other things, support our immune function, assist with digestion and nutrient absorption, boost our cognitive function, and even regulate our moods. As adults, this vast ecosystem consists of nearly 100 trillion microscopic organisms living in and on our body.

Babies aren’t born with mature microbial colonies, though—they are just beginning to establish this wondrous world of bacteria. The good news is that, developed correctly, their microbiome lays the foundation for a lifetime of optimal and vibrant health.

Why is the Microbiome So Important?

The vast majority of bacteria in our microbiome live in our gut, where 80% of our immune system resides. In a properly balanced microbiome, the good guy bacteria will crowd out the bad guys and help to regulate the immune system so that it doesn’t overreact or underreact to stimuli. Because babies are born without a mature immune system, they depend on the proper colonization of microbes for optimum immune function.

Probiotics, the good microbes, also help to protect the gut barrier against toxins and harmful invaders, which is especially important for an infant’s “open” gut1. For the first 4-6 months of life, babies have spaces between their intestinal cells that give direct access to the bloodstream. Good bacteria stabilize the intestinal barrier and help to fill in the gaps, so undesirable molecules are less likely to slip through.

Beneficial bacteria also help to make sure babies can properly absorb valuable nutrients from the foods they eat and drink. Some good microbes even produce vitamins, like B and K, that are integral to a baby’s rapid growth!

It’s clear that a balanced microbiome is critical for good health, but how exactly does the microbiome develop?

Timeline of the Microbiome

An infant’s microbiome is mostly sterile in the womb and then continues to mature up until about age 3, when it starts to resemble the bacterial composition of an adult microbiome.

Microbiome development follows several general stages:

Scientists used to think the microbiome was sterile until birth, but new research shows that babies are exposed to their mom’s bacteria in the placenta, which harbors a variety of microbes (some of which originate in the mouth, which is why prenatal oral health is so important!)2.

During Delivery
As soon as mom’s water breaks (goodbye bacterial barrier!) and the baby begins to descend through the birth canal, they begin to pick up vaginal bacteria—these become baby’s first mass colonizers that set the stage for proper growth and development. However, the mode of delivery makes a drastic difference in the types of bacteria that begin to settle into baby’s gut. Babies delivered via Cesarean section tend to have different, less beneficial bacterial colonies, which may be why C-section births are linked with various long-term health challenges3.

After birth is when your baby’s microbiome colonization really continues to ramp up. Right away (within minutes, hopefully), skin-to-skin contact will transfer some of your valuable skin microbes directly to your baby, where they can get to work protecting your baby’s largest organ. Indeed, skin microbes display antimicrobial properties that can ward off inhospitable bacteria4.

Within hours, your breast milk—chock full of friendly bacteria that make their way into your baby’s body for optimal microbe inoculation—can get to work seeding your baby’s microbiome. Full of nutrients, growth factors, and vitamins, breast milk is the perfect food for your baby and your baby’s microbes.

0 to 6 months
Breastfeeding exclusively until six months of age creates the perfect environment for proliferation of the good bacteria that work hard to develop your baby’s immune system to keep them healthy. HMO’s (milk sugars) in breast milk selectively feed the beneficial microbes so they can thrive and grow.

6 months and beyond
As you begin to introduce solid foods to your baby’s diet, the microbiome starts to shift from a simple, Bifidobacteria-rich environment full of bacteria that digest milk sugar to a more diverse one with species that can break down starches and complex sugars to accommodate your baby’s new menu. By around age 3, your toddler’s gut is much like your own in terms of variety of bacteria.

Building a Strong Infant Microbiome

Since a baby is born with a nearly sterile gut, they depend on their mom’s beneficial bacteria to kickstart their own microbiome. The bad news is that without the right microbial mix, their immune system may not develop correctly, leading to a host of long-term health problems.

As moms, we can’t always control how our babies are born, but we can make choices before and after birth that can help seed our baby’s microbiome in the best way possible.

1. Focus on yourself. Making sure you have a healthy microbiome before, during, and after pregnancy is the key to being able to pass the same on to your baby. Do your best to stay away from things that deplete your gut health like stress, processed foods, antibiotics, and medications while focusing on exercise, relaxation, and a whole-foods diet. Taking a daily high-quality probiotic formula like PRO-Moms will also help you seed your own microbiome with tons of good bacteria to pass on to your little one.

What’s more, research shows that taking a probiotic while pregnant supports you and your baby by strengthening your immune system, supporting healthy glucose levels, reducing the dreaded pregnancy-related constipation, producing folate (the non-synthetic version of folic acid), promoting proper nutrient absorption, and supporting more balanced mental and emotional function.

And the benefits don’t stop when you deliver! Continuing to nurture your microbiome by taking probiotics postpartum will help reduce the baby blues, help you shed the baby weight more quickly, and make sure that your breast milk is optimized with plenty of beneficial bacteria for your baby. And we know that when a baby has a healthy microbial start, they are more likely to have a strong immune system, balanced metabolism, and proper brain and cognitive development, all of which can last a lifetime.

2. Find supportive caregivers. As soon as possible, seek out an OBGYN, Midwife and/or Pediatrician who understands the importance of supporting your child's gut health. Information on the infant microbiome is relatively new and you’ll want to find a partner in health who can help you make the best decisions for your family. In addition, find out where your practitioner stands on interventions. Many of our modern day medical interventions aren't medically necessary and we are now learning that they can be detrimental to our colonies of good flora, leading to health consequences down the road.

3. Deliver as naturally as possible. Sometimes a Cesarean section is necessary, and you would never want to compromise your baby’s health by refusing one in an emergency. But if you have the choice, a vaginal birth is the best way to slather your baby with good bacteria. If a C-section is inevitable, vaginal swabbing may help restore the vaginal bacteria usually acquired during childbirth. One study showed that vaginal swabbing right after birth gave babies delivered via Cesarean microbiome profiles similar to vaginally delivered babies5.

Also, make to sure avoid any unnecessary antibiotics before and after delivery (both for yourself and your baby), as these can wipe out the good bacteria that are trying so hard to colonize in your baby’s gut.

4. Breastfeed, breastfeed, breastfeed. Make no mistake—breastfeeding is possibly the most powerful tool in your toolbox when it comes to giving your baby the best microbial start at life. Feeding your baby only breast milk for 6 months maintains your baby’s “virgin gut” and is the best way to make sure your baby is getting all of the good flora they need for immune system development. And by exclusive breastfeeding, we mean nothing else—no water, juice, food, or formula. Studies show that exclusively breastfed babies have healthier microbiomes than formula-fed infants and that introducing any formula changes the microbiome quickly6.

5. Choose healthy solids. Once it’s time to start introducing solids, focus on nutrient-rich foods that will help them (and their microbes) grow and develop. Providing organic, whole food fruits and vegetables that are high in prebiotic (food for bacteria) fibers will give the good guys in your baby’s gut everything they need to thrive for optimal immune system development. Fermented foods like sauerkraut can also boost your baby’s probiotic population exponentially!

As you navigate the first couple years of your baby’s life—showering them with love, affection, and plenty of kisses—don’t forget to nurture their inner microbial world, too! By giving the microscopically tiny friends in your baby’s microbiome all they need to thrive, you’ll be setting up your precious little one for lifelong health and happiness.

1. Rao, R. K., & Samak, G. (2013). Protection and Restitution of Gut Barrier by Probiotics: Nutritional and Clinical Implications. Current Nutrition & Food Science, 9(2), 99-107.
2. Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014). The Placenta Harbors a Unique Microbiome. Science Translational Medicine, 6(237).
3. Blustein, J., & Liu, J. (2015). Time to consider the risks of caesarean delivery for long term child health. BMJ, 350(Jun09 3).
4. Christensen, G., & Brüggemann, H. (2014). Bacterial skin commensals and their role as host guardians. Beneficial Microbes, 5(2), 201-215.
5. Dominguez-Bello, M. G., Jesus-Laboy, K. M., Shen, N., Cox, L. M., Amir, A., Gonzalez, A., . . . Clemente, J. C. (2016). Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine, 22(3), 250-253.
6. Madan, J. C., Hoen, A. G., Lundgren, S. N., Farzan, S. F., Cottingham, K. L., Morrison, H. G., . . . Karagas, M. R. (2016). Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA Pediatrics, 170(3), 212.


Emily Courtney is a Writer and Editor at Hyperbiotics and mom to two fun and active boys. Emily is passionate about natural wellness and helping others learn about the power of probiotics for vibrant health! For more ideas on how you can benefit from the power of probiotics and live healthier days, be sure to subscribe to our newsletter.

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Posted in Infant & Toddler Health, Mom + Child, Pregnancy & Breastfeeding