Building your Babe's Microbiome


The microbiome is seemingly miraculous. It works to support immune functioning, assist with digestion and nutrient absorption, boost cognitive functioning, and regulate mood. These vital functions are essential to human health.

An adult microbiome is composed of nearly 100 trillion microscopic organisms weighing 4-6 pounds, living in and on our bodies. Humans are not born with mature microbial colonies. Rather, through the mother before and during pregnancy, vaginal birth (or vaginal seeding), and breastfeeding, an infant’s microbiome is established.

If properly developed, the microbiome lays the foundation for a lifetime of vibrant health. If disrupted, inflammatory conditions including allergies, food intolerances, eczema, asthma, and autoimmune disorders can develop.

It’s essential to understand how to build a healthy microbiome for both you and your baby. The following suggestions will guide you through the development of an optimal microbiome in your child, beginning from before conception through to birth and beyond.


It was previously believed that fetuses are completely sterile in the womb and are only first exposed to bacteria during vaginal birth. It has now been discovered that babies in the womb are exposed to their mothers’ bacteria through the placenta, which harbors a variety of microbes.

Since the fetus is exposed to bacteria from the time of conception, it’s crucial that the mother has a healthy microbiome before conceiving, during pregnancy, and post-pregnancy while breastfeeding to ensure she is able to pass the same onto her baby.

An excellent way a mother can cultivate a healthy microbiome that has balanced levels of good and bad bacteria is by taking a probiotic beginning 3-6 months before conception. Supplementing with a probiotic will support a mother and her baby by strengthening the immune system, supporting healthy glucose levels, reducing constipation, supporting the production of folate, promoting proper nutrient absorption, and supporting more balanced mental and emotional functioning. Additionally, taking a probiotic from the beginning of pregnancy can play a role in preventing preterm birth, urinary tract infections, and Group B Streptococcus (strep) infections. While taking a probiotic earlier is ideal, the baby and mother will still gain many health benefits from beginning a probiotic in the 3rd trimester. A mother will have lower rates of atopic conditions, including eczema and allergies, especially in the event of a cesarean section.

Aim for a probiotic with a minimum of 15 billion CFUs and a maximum of 100 CFUs daily in any product. It’s helpful to gradually introduce probiotics over a 2 week period as your body adjusts, and similarly to increase the number of CFU's over time.

Fermented foods should also be eaten daily by women who are pregnant or trying to conceive. Fermented foods will ensure proper digestion and absorption of nutrients, provide the baby with B vitamins and vitamin K, and will enhance good bacteria in the gut.

In addition to regularly consuming probiotics and fermented foods, keep the following in mind:

Eating a fiber-rich diet will further support a healthy microbiome. Fiber increases the diversity of the bacteria that live in the mother’s intestines (or “gut”). As a byproduct of their metabolism, fiber-loving bacteria, fungi, and other bugs produce acetate and butyrate, which are two compounds that help strengthen and maintain the gut barrier. This barrier exists between the intestines and the bloodstream. Protecting it lowers the risk of developing autoimmune conditions. The bacteria gathered from consuming fiber-rich foods will help the mother pass healthy microbes to her baby during pregnancy, delivery, and through breast milk.

Consuming prebiotics are also beneficial as they act as food for the healthy bacteria in your microbiota. If taking a probiotic or eating probiotic foods, they will flourish and remain in the gut (rather than be excreted) if they have prebiotics to feed on.

Prebiotic-rich foods include: sweet potatoes, oats, bananas, onions, raw garlic, and raw chicory root.

All pregnant women should avoid processed foods (anything that comes in a box, package, or can), soft drinks, refined sugar, and food additives. These foods feed bad bacteria, which can lead to a slew of negative health outcomes.

Focus on consuming: savory, whole foods, including a variety of vegetables, organic grass-fed meats, small wild-caught fish (such as sardines and anchovies), organic pastured eggs, and foods containing healthy natural fats like nuts, seeds & avocados. Sweet foods should be consumed as snacks (as they can cause digestion issues when combined with heavier meals) and should generally consist of fruits like berries, apples, and pears.

What about antibiotics? Sometimes antibiotics are necessary and potentially life-saving. Some infections, such as UTIs, require antibiotics for the safest treatment during pregnancy.

If antibiotic use is necessary, the mother should take a probiotic supplement along with the antibiotic (taken at least an hour apart) and continue with the probiotic until after pregnancy. It’s important not to worry or stress too much about taking an antibiotic. Many expecting mothers will have to, and no negative effects have been shown.


During a natural vaginal birth, the baby begins to descend through the birth canal when the mother’s water breaks, picking up vaginal bacteria as is leaves its mother’s body. The bacteria it is exposed to head-to-toe during a vaginal birth are the baby’s first mass colonizers that will set the foundation of its future growth, development, and overall health.

Sometimes a cesarean section is necessary, and in the case of such an emergency you must do what is best for your and your baby’s health. This does mean, however, that the baby will be delivered under sterile surgical conditions through their mother’s lower abdomen. This difference has a profound impact on gut colonization. The subsequent changes in the baby’s microbiome will put them at a higher risk for obesity, allergies, and type 1 diabetes.

To counteract the effects of a sterile birth, “vaginal swabbing” or microbiome seeding has shown promising benefits in helping to partially restore the flora of C-section babes. If the doctors predict a C-section will be absolutely necessary, the procedure for vaginal swabbing can be requested. A sterile gauze is folded into a fan shape, moistened with sterile water, and inserted into the vagina. It’s then left in there to colonize for one hour. The gauze is then removed and put into a sealed bag until the baby is born. At birth, the gauze is wiped over the baby’s face to mimic the passage through the birth canal. This process remains controversial among the medical community. While the oral and skin microbiome of the baby will be positively impacted, it has not been confirmed whether this process has long-term effects on the gut microbiome of the baby.

While critics raise valuable points, so long as the mother is tested for harmful microbes before swabbing and is confirmed negative, the process is a potentially valuable stop-gap method for when cesarean is needed.


After birth, the infant’s microbiome colonization continues to grow at high rates. Right away (within minutes, hopefully), skin-to-skin contact will transfer some of the mother’s valuable skin microbes directly to the baby, where they can get to work protecting the baby’s largest organ. Skin microbes display antimicrobial properties that can ward off bad microbes.

Within hours of birth, the mother will ideally breastfeed for the first time. Breast milk is composed of high amounts of healthy bacteria that will enter the baby and continue microbe inoculation. Additionally, it also contains nutrients, growth factors, and vitamins. Breast milk is the perfect food for your baby and your baby’s microbes.

Continuing to nurture your microbiome by taking probiotics postpartum will help reduce postpartum depression and mood disorders, enhance weight loss, and ensure that breast milk is optimized with plenty of beneficial bacteria for the baby. You can also supplement breastmilk with probiotic supplements and continue to do so for six months. There are two easy ways to give a baby probiotic supplements, if necessary. The first and most effective way is to mix probiotic powder into a couple of tablespoons of breast milk and put the mixture in an eyedropper. Then you can either put the dropper next to your nipple while nursing or give it to your baby directly from the dropper between nursings. The other way is to put the probiotic powder into a clean dish or surface and dip a clean finger into the powder. You can let baby take it off your finger until the full dose has been taken.

When a baby has a healthy microbial start, they’re more likely to have a strong immune system, balanced metabolism, and proper brain and cognitive development, all of which are benefits that last an entire lifetime.

0-6 Months

Breastfeeding exclusively until six months of age creates an ideal environment for proliferation of the good bacteria that are required to develop the baby’s immune system. Exclusive breastfeeding means that the baby consumes nothing else, including water, juice, food, or formula. Breast milk contains a sugar called human milk oligosaccharides (HMOs). HMOs feed the initial colonization of microbes in a baby’s gut, mainly the Bifidobacterium infantis. B. infantis is known to support brain development, folate production, immune support, and most importantly to feed an infant’s gut cells to begin the process of sealing their naturally-permeable (leaky) gut. These HMOs and probiotics are responsible for optimal long-term health of a newborn.

*If you are unable to produce breast milk- reach out to a lactation specialist & holistic practitioner for support. You can also look for donor milk, if this is something you feel comfortable doing. 

Avoid any unnecessary antibiotics. When needed, antibiotics can be live-saving, as mentioned previously. However, antibiotics are often over-prescribed. They’re given for mild illnesses that would resolve on their own and for viral illnesses, like the common cold and most ear infections, against which they are completely ineffective. Antibiotics are harmful to the gut because they can diminish overall species diversity, devastate commensal gut bacteria that benefit our health, and open the door for infections caused by bacteria, such as C. difficile.

Check with your doctor and cross check with your holistic practitioner to ensure an antibiotic is truly necessary, and if it is, support your baby with breast milk and probiotic supplements.

6 Months +

At six months, a baby can be introduced to solid foods. This is because when born, a baby’s microbiome can only digest milk sugars but as the microbiome diversifies, it can begin to break down starches and complex sugars. By the age of 3 years, a child’s microbiome looks almost identical to an adult’s.

Nutrient-rich foods that help the child and their microbes grow and develop should be the focus during solid food introduction.

The most beneficial foods include: organic whole fruits and vegetables, prebiotic foods, and fiber-rich foods. Fermented foods, such as sauerkraut, kefir, kimchi, and miso, can also significantly boost your child’s probiotic population.

Other helpful tips include:

  • Starting your baby with bone broths or herbal broths

  • Using very little grains at first

  • Building a wide palate with a variety of vegetables vs. only using sweet veggies & fruits

There’s no quick & easy way to develop a baby’s microbiome - it’s truly a holistic practice that begins before the baby is even born and continues for a lifetime. Following this guide will help your baby build a healthy & strong gut.