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Does a Newborn Baby Have its Own Microbiome?

The human microbiome—comprised of bacteria scattered throughout the body — is truly amazing. The microbiome has been the subject of an extensive amount of research and analysis in recent years, especially its presence and activity within the gut. Studies have shown that the microbiome directly affects our overall health and well-being, starting with the very first moments of life.

Many mothers-to-be understandably place a lot of focus on planning the best possible birth for their babies, yet one of the most commonly overlooked elements of birth is how it affects an infant’s microbiome. This major debate lies in the differences between a vaginal birth and Cesarean section, both of which can extensively mold not only the formation of the child’s microbiome, but also his or her overall health later in life.

Pregnancy and Bacteria: A Symbiotic Relationship

As soon as a woman becomes pregnant, numerous changes begin to happen within her body. Aside from the most commonly referenced effects of pregnancy such as weight gain, nausea and fatigue, rather significant changes begin to occur with the microflora balance both in her and entire body. These changes tend to be miniscule throughout the first trimester of pregnancy but speeds up significantly with the approach of the third trimester, as pregnancy progresses.

The body’s balance of bacteria changes in ways that are reminiscent not of a good picture of overall health, but rather more closely aligned to someone who suffers from diabetes. Inflammation increases throughout the body, along with a dramatic reduction in insulin sensitivity. Fortunately, such changes are temporary and serve the key purpose of supporting the growth and nourishment of the fetus.

Unsurprisingly, a mother’s microbiome has a major influence over the microbiome of her newborn, as the vast majority of these bacteria are obtained during birth and from breastfeeding. However, it is the method of birth that has been getting keen attention lately due to the overall effects it seems to have on a newborn’s microbiome.

Vaginal Birth vs. C-section: The Effects on the Microbiome

There are a variety of reasons why a woman might consider C-section birth, which continues to be on the rise throughout the world. In many cases, a Cesarean Section will be either recommended or necessary for supporting the health of either baby, mother or both. Often, however, it’s a function of choice after weighing the pros and cons of each delivery method.

A consideration to undergo natural, vaginal childbirth over C-section is how the baby’s microbiome is affected. During vaginal birth, the infant rubs against the mucosal lining of the birth canal, exposing it to a wide range of different bacteria that effectively “colonize” its very own microbiome, even before delivery occurs.

Often referred to as “seeding the microbiome,” the process continues well after birth via skin-to-skin contact, which offers an additional layer of padding to the child’s delicate balance of microflora. While this process helps to bolster the skin microbiome, breastfeeding allows the child to receive large amounts of beneficial gut bacteria — a key element of keeping harmful pathogens at bay early in life.

With a C-section, the end result can be quite a bit different. Because the baby travels from a sterile environment within the uterus to an even more sterile hospital environment with Cesarean birth, the initial “seeding” of the microbiome with beneficial bacteria never occurs. The child receives none of the millions of diverse bacteria typical of vaginal birth and thus relies upon breastfeeding and skin-to-skin contact as tools for building a healthy microbiome.

Possible Effects Later in Life

There are numerous reasons why experts believe it is important for a child to be born with the initial stages of a robust, diverse microbiome. Much of this comes down to the importance of maintaining a healthy balance of “good” and “bad” bacteria throughout the body, the ratio of which should be approximately 85% to 15% respectively. When a newborn enters the world with an imbalanced or incomplete microbiome, he or she is set up for numerous potential hurdles that can lead to health problems down the road.

For one, balance in the human microbiome is essential to building and maintaining immunity. When harmful bacteria overwhelm the beneficial microbes that help support the immune system (70% of which lives within the gut), inflammation tends to result, as does a reduction in defenses against viruses such as the flu and common cold – immune dysfunction. This may lead to more sickness early in life but could potentially also contribute to immune system problems as the child grows through puberty and into adulthood.

Additionally, an imbalanced microbiome in a newborn may impede his or her ability to properly digest food and absorb nutrients. Beneficial microflora are instrumental in assisting in this process, and when they’re not present in large enough numbers, gastrointestinal insufficiency can result in infancy with a higher risk of GI issues throughout life.

Research has even shown indications that there may be links between Cesarean Section birth and non-communicable diseases such as allergies and asthma. Though further analysis is required to better understand the connection between these two factors, both have been on the rise in recent years. This link is just one more case for choosing vaginal birth if the option is deemed medically safe, and a development that is likely to see quite a bit more research in the coming years.

For those women who do not have the option, however, extra focus should be placed on the importance of breastfeeding and skin-to-skin contact. Methods such as Kangaroo Mother Care, for example, can not only assist in building the child’s microbiome, but are also essential for helping to build the connection between mother and child.

Boosting a Newborn's Microbiome

As newborns gain so much of their initial start from the microbiome from their mothers, it is clear why the health of the mother’s microbiome matters so much. This is important before pregnancy, during (when balance will naturally be thrown off due to normal changes within the body) and after—especially if the child will be breast-fed. The more beneficial bacteria that can be delivered to the child both prior and post-birth, the better.

Looking to boost your newborn’s microbiome? Here are just a few steps you can take before, during and after your pregnancy:

Start with Probiotics

The first step in helping to support a healthy ratio of good/bad bacteria for your newborn is to work on raising numbers of your own beneficial bacteria—especially since pregnancy itself can cause imbalance. By taking probiotics (especially as soon as you become pregnant), you’ll be adding helpful microflora to your gut, skin and vaginal canal—all of which will serve to “seed” your newborn’s microbiome.

Additionally, you may want to continue taking probiotics well after your pregnancy has ended. It can take some time for postnatal effects on the body to subside, and the more balance you have within your own microflora, the more you’ll be able to contribute to your infant.

Be Gentle

A newborn’s skin is incredibly sensitive and subject to irritation, which is why it’s recommended to bathe him or her using extremely gentle soaps for at least the first few weeks. This is because the newborn’s skin lacks the oils, bacteria and natural peptides found on the surface of more mature skin. When it comes to interfering with this process, less is more. Be sure to also stick with soft, gentle materials when choosing clothing and bedding.


Breastfeeding is, without a doubt, one of the best methods of transferring beneficial microbes to a baby’s microbiome. There’s evidence that it may even be an effective way to combat microflora loss from antibiotic use. Numerous additional benefits are associated with breastfeeding when compared to formula, not to mention the skin-to-skin contact.

Snuggle Up!

Hugging, kissing and snuggling with an infant is a potent way for mother and child to grow a connection with one another, but its benefits extend beyond that. Every time you cuddle with your newborn, you transfer a diversity of healthy microbes from your skin and saliva. The end result? A more diverse microbiome for your baby, as well as a connection that will last a lifetime.
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