• Allison Fahrenbach


Updated: Jul 15

Before you even entered into this world, conditions were set up for your growth and development. This includes a healthy microbiome.

The gut microbiome should be thought of as an organ system that has important effects on childhood development. Features of the intestinal microbiota can affect the development of the brain, immune system, and lungs, as well as body growth. Dysbiosis has been associated with disease development in children and adults, including autism, attention deficit hyperactivity disorder, asthma, and allergies.

But how and where does the microbiome originate? What shapes our microbiome in the womb, and outside of it?

In this blog I’ll discuss how the microbiome develops before birth, during birth, and in infancy as well as share factors that may support or hinder healthy microbiome development as we age.


The establishment of the gut microbiome actually starts before birth.

Even prior to conception, the condition of a mother’s own gut health can impact the health and development of her baby.

During pregnancy, most organ systems change to promote healthy gestation

and prepare for birth. This includes the mother’s microbiome, which shifts throughout pregnancy to create a more optimal microbiota blend for her baby.

When a woman becomes pregnant the diversity of microbes within her gut actually starts to decline. During the first trimester, there is a shift in the composition of gut flora; microbes during this time are predominantly Firmicutes – mainly Clostridiales – and there is a decrease in the number of Bacteroidetes.

But by the third trimester the microbiome shifts into the profile of an obese or highly inflammatory community. From the first to the third trimester, Proteobacteria, Bifidobacteria, and bacteria producing lactic acid increase.

These changes, combined with metabolic and hormonal changes, set up a situation that may induce weight gain and affect metabolism in order to provide a sufficient energy supply to the fetus.

Even a woman’s immune system shifts during pregnancy. During pregnancy the mother’s immune system is actually suppressed so that her body doesn’t “mistake” her baby for a foreign invader. This is one reason expectant mothers are encouraged to avoid foods like sushi and soft cheese which naturally can carry more pathogenic bacteria.

For decades, it was widely believed that the womb, along with the placenta that nourishes the fetus, was a sterile environment, and therefore babies were “sterile” until born. But recent science shows evidence of microbial communities existing in the umbilical cord, amniotic fluid, and placenta. This suggests that colonization of the baby’s microbiome actually begins in the womb.

Maternal gut organisms have been identified in the meconium (the initial substance present in the intestines of a fetus), which supports the notion that placental microbiomes may be where babies first encounter the microbial world. Some studies have suggested that the presence of these placental microbiomes is the result of contamination, or a sign of infection.

Its uncertain exactly how these microbes enter the intrauterine space, but it is believed that bacteria is transmitted from the mother by moving from her gut, passing into the bloodstream, and making its way to the placenta or amniotic fluid (which the baby can swallow).

What we do know is that the environment of the womb and the health of the mother’s microbiome does impact the development of her baby’s microbiome.

A compromised microbiome (dysbiosis) during pregnancy may increase the risk for certain complications, including preeclampsia, preterm birth, and gestational diabetes, and impact the health of the baby. On the other hand a balanced microbiome can help build a strong foundation for the baby’s own gut health.

Prenatal development of the microbiome can be affected by several factors. Things like the mothers diet, if she smokes, is obese, and antibiotic use during pregnancy can all impact the composition and development of infant gut microbiota.

Luckily, there are many opportunities to help improve gut health and support the microbiome’s healthy development, such as following a balanced and nutritious diet, maintaining a healthy pregnancy weight, engaging in regular exercise, managing stress, abstaining from alcohol consumption and smoking, and consuming fermented foods.

Probiotic therapy (supplements) can also help improve gut health, but understanding the various strains is important to ensure the appropriate formulation (strain or combination of strains), and the proper dosage, is taken.

Pregnant women should consult with a health practitioner to confirm what type and dosage of probiotic (if any) is best for them and should likely undergo testing first so their individual microbial composition can be assessed prior to using any probiotic.


Newborn babies experience rapid colonization of microbes at the time of birth, continuing into the their first year of life, from both the mother and the surrounding environment.

Infant microbiota is shaped by three main factors:

  1. The birth process (vaginal or c section)

  2. Diet (including breast milk and the diet of the mother)

  3. Antibiotics or other environmental disturbances

Let’s start with the birth process. How the baby is delivered plays a crucial role in establishing the infant gut microbiota.

With a full-term vaginal delivery, the newborn comes out covered in bacteria, mainly Lactobacillus. This is the predominant bacteria in the mother’s vagina and it can survive oxygen.

The child also comes out face down so it acquires bacteria from the mother’s anus.

This exposure to different bacteria may allow for a more diverse array of microbes, which can be key to creating a healthier and more disease-resistant system for the newborn.

I know this image isn’t the most appealing to think of, but this is exactly what nature intended so the baby can begin developing its own community of beneficial bacteria.

The initial bacteria that populate the microbiome are called “facultative anaerobes.” These bacteria can handle oxygen but quickly switch to the fermentation process. The reason for this is that a baby’s gut contains oxygen. The first bacteria have the job of consuming that oxygen.

This is - of course- assuming a vaginal delivery. But in the US 1/3 of all babies are born via cesarean section (C-section). C sections provide the first alteration to a baby’s microbiome.

A child born via c section comes out covered in more Proteobacteria (mostly Staphylococcus and Acinetobacter) and less Bifidobacterium.

It may be that the baby picks up bacteria from the skin of the mother, from the delivery room, or any other bacteria nearby as these are common bacteria from those areas and bacteria are- literally- everywhere. So when it’s not handed down from the mother through the natural birth process the baby acquires whatever bacteria is in the vicinity to make up for it.

Birth via c section may result in a predisposition for or increase in certain health issues, such as obesity, type 1 diabetes, celiac disease, or allergies. This is because C-sections unfortunately do not give the baby the opportunity to ingest maternal microbiota from the vagina or colon.

This has led researchers to believe this could partly be due to the bacteria the baby is missing out on when it doesn’t take a natural journey through the birth canal.

In no way is this meant to vilify c section births. C sections have saved many babies and mothers over the years. The point is to explore the value and wisdom behind natural birth so we can look for alternatives and replacements for this bacteria when natural birth isn’t an option.

One process is what’s known as “vaginal seeding” or “microbirthing”. This process involves a doctor placing gauze swabs in the mothers vagina, which then get rubbed all over the baby’s face and body when they’re delivered via c section. The goal is to give the baby the same bacteria that they would naturally get having been born vaginally.

The degree of effectiveness is yet to be determined and it’s a controversial practice. The American College of Obstetricians and Gynecologists (ACOG) actually opposes it.

And some research has indicated that while vaginally born and C section-delivered babies do have very different microbiomes, this difference is likely due to the antibiotics that are administered before a C-section, not vaginal bacteria. These antibiotics can cross the placenta to the baby, wiping out their microbes.

To help optimize the microbiome of a c section born baby:

Breastfeed. About 30% of the beneficial bacteria in a baby’s tummy come from breast milk.

Skin-to-skin contact with a baby right after birth. About 10% of your baby’s good bacteria come from the skin around the breasts.

Delaying the baby’s first bath for 12 hours.

Avoiding unnecessary antibiotics.

Once the baby is outside the mother, there will continue to be further exposure to bacteria – for example, the first skin-to-skin contact with the surrounding environment (delivery room, home, etc.), nursing procedures, and contact with other individuals.

Many new parents can be anxious about their baby coming into contact with germs at this time, especially while the immune system is still maturing during the first 2–3 weeks of life.

However, generally speaking, early exposure to bacteria and certain allergens within the first year can have positive effects on the baby’s immune responses.

For example, babies exposed to dander and a variety of household bacteria seem less likely to suffer from allergies and asthma. (NOTE: the timing of initial exposure is key. In these studies, no protective effects of exposure were seen if the initial encounter occurred after one year of age.

Most often, this exposure will occur naturally, so it isn’t necessary to deliberately expose your baby to germs; once a baby is older than 8 weeks, parents can be less anxious about protecting the child from contact or exposure to healthy visitors.


The microbiome development is primarily disrupted by three things; C-section births, perinatal antibiotics, and formula feeding.

So with the introduction of feeding, there is another opportunity to positively impact microbial development.

Breast milk contains bacteria, hormones, and antibodies that have properties to meet a baby’s nutritional needs and developing immune system. It has been estimated that 25–30% of the infant bacterial microbiota originates from breast milk.

Beneficial bacteria also exists on the skin of the mother’s breast.

For these reasons, between the ages of 3 and 18 months, at least partial breastfeeding is shown to have a significant relationship to the variance in the baby’s gut microbiome.

It’s also worth mentioning that growth is also significantly greater in breast-fed compared to formula-fed preterm infants following their discharge from hospital.

So the impact of breastfeeding on infant microbiota may also enhance the baby’s growth and developmental pathways.

The next important transition occurs during the weaning period when breastfeeding continues, but solid foods are also introduced.

The introduction of new foods brings on a more complex and diverse gut microbiome and this period from (6 months to 2 years of age) represents a crucial period for child growth.

On the other hand, under-nutrition in this period- or even improper nutrition- may perturb the intertwining gut microbial and growth pathways.

Whole foods that are rich in dietary fiber and protein may create an environment that promotes specific microbes to establish in the gut that will build beneficial diversity.

One study suggests that oatmeal, rich in dietary fibers that can be utilized by gut microbes, is one of the best foods to promote microbial diversity during this time.

The timing of food introduction is also important. If too much diversity is created too early, it can be problematic. For this reason, parents should not introduce solid foods prior to three months of age.

Further development then occurs when breastfeeding stops completely. This helps accelerate the microbiome’s maturation, which in turn leads to a more stable microbiota.

This phase, which continues until about the age of three, also marks the introduction of table food. This is when the intestinal microbiome begins to resemble that of an adult intestine.

During this time, after breastfeeding has stopped, the introduction of foods like cheese, rye bread, and meat may be advantageous for promoting microbial diversity.

Of course, any foods or food groups that a child has a sensitivity or allergy to should be avoided. Ultimately, bio-individuality will determine what foods do and do not work.


While the gut continues to develop into childhood, it is the period of initial microbiome development – which has been connected to brain development, allergies, and obesity – that truly lays the foundation for health throughout one’s life.

Its usually in adolescence that we begin yo see the impact of those formative years start to unfold.

At the same time, childhood presents a great opportunity for healthy eating habits to be established with help and education from parents and caretakers.

There are many ways to support the health and diversity of a child’s microbiome:

1| Be mindful about the use of antibiotics: As a parent, you may want to consider discussing the necessity of prescribed antibiotics with your child’s healthcare provider. If possible seek alternative options to antibiotics and if antibiotics are absolutely necessary, you may want to discuss probiotic therapy.

2| Feed developing microbiomes well: Childhood nutrition is incredibly important. Encourage the acceptance of gut-nourishing foods by getting creative with a variety of colorful fruits, vegetables, whole grains and fermented foods.

You can increase the variety of fruits and vegetables eaten by letting lids pick a new fruit or veggie to try each week. Prepare them in several ways (raw, roasted, or steamed) and don’t be afraid to let children play with their food – cut-up fruits and veggies make great edible art projects!

Child-friendly fermented foods to add to the menu include yogurt and/or kefir with live active cultures. Serve them alone, in smoothies, or as an alternative to milk on cereal.

Emphasizing these foods will help crowd out less gut-friendly choices, such as those full of artificial ingredients, refined grains, or added sugar.

Keep in mind there is no need to worry about every single food choice a child makes. It is important to let kids be kids and strictly banishing all sugar and processed foods may even encourage children to seek out those foods even more.

A balanced approach is always best.

It’s all about doing what you can and making strides to support a child’s gut microbiome within the overall big picture of health.

3| Play in the dirt: Beneficial bacteria are abundant in soil – in fact, one teaspoon contains almost one billion bacteria!

Exposure to soil bacteria and rural environments has been linked to anti-inflammatory and immune health benefits. Children raised rurally age with more resilient and robust immune systems, thought largely to be the result of early exposure to bacteria in the soil and dirt.

Kids who play in dirt face exposure to germs and parasites that can help reduce risks of suffering certain allergies and illnesses later in life. Early microbial exposures help our bodies to learn how to regulate inflammation.

As an aside, there’s also a lot of studies that indicate that playing outdoors and getting dirty also decreases stress and anxiety in children.

In a lab study using mice, researchers at the University of Bristol and their colleagues at University College London found that exposure to certain commensal bacteria found in soil altered behavior in much the same way man-made chemical ingredients do in anti-depressant drugs.

As we grow older, many elements continue to influence the bacteria in the gut, including stress, diet, alcohol and drug consumption, smoking, sleep, antibiotic use, and what we are or are not exposed to in our environment. As adults, what we eat and drink, how we manage stress, and how we take care of ourselves can all impact and change our microbiome, for better or for worse.


It is helpful to understand the typical trajectory for optimal development of the microbiome. It can allow for insight and understanding as to what has shaped your own microbial balance, and, if you are a parent or soon-to-be parent it can help you to make informed decisions.

However, there is no one-size-fits-all approach to pregnancy, birthing, and child rearing that guarantees specific health outcomes.

The circumstances and personal decisions which dictate whether babies are born vaginally or via C-section and breast-fed or formula-fed are unique to each family. And in many instances parents may not have a choice in how a child is delivered or fed.

When vaginal births may not be an option, C-sections are necessary.

If a baby is unable to latch on to the breast, formula may be the only viable alternative.

So while it’s important to understand what set of circumstances can optimally shape the microbiome, it’s equally as important to not pass judgment if- for one reason or another- those optimal circumstances were not an option.

While the early years of microbiome development set the stage for gut health later in life, there is so much you can do to improve the health of your microbiome in adulthood regardless as to what happened or didn’t happen to you as a child.

Even if the early stages of development were not ideal, there is always an opportunity to turn things around. We make dozens of decisions daily that impact our gut- for better or for worse- so even if your infant microbial development wasn’t the best, your adult years afford your with plenty of chances to improve it!

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