"If we miss the window at birth, then the immune system never matures correctly. If you upset this process in early life, then we may have consequences later. That can lead to the development of disease later in life."
-Dr. Rodney Dietert, Professor Emeritus of
Immunotoxicology, Cornell University
Human kind has co-evolved over the last four million years with our microbiome physiology communities located in multiple body sites. Yet, there is much more to learn about how an infant is first exposed to and colonized by them. But we do believe that having an understanding of their characteristics has everything to do with human development and physiology—which makes this a current, rich, evolving, and fascinating field of study and research for those interested in childbirth!
There is general agreement among scientists and experts that a healthy microbiome strengthens a baby’s immune system and significantly impacts our health as adults. We cannot live without our microbiome. Always remember that our health is our wealth.
Our Microbiome
The microbiome refers to all the hundred trillion forms of bacteria, viruses, fungi, protozoa, and their genes that live in every nook and cranny inside of us and around us in the water, soil, and air. These microorganisms are too small to be seen by the naked eye. They form an eco-community that is inextricably tied to our health. For example, how to comprehend that in just one drop of fluid from the human colon (at the end of the digestive system), we can find one billion bacteria?
Where do they come from, what do they do, and why can’t we live without them is a gradually unfolding mystery. Of the many, we now understand that most are important for our health, and they live in harmony with us as human hosts, providing vital functions essential for human survival. This is a newer understanding because some do make us sick. It was only since 2008, when the National Institutes of Health studied their genetic code, that we learned not all bacteria cause illness—in fact, most bacteria benefit health. The good ones prevent bad pathogenic bacteria and help us to digest nutrients, synthesize vitamins, and support the immune system in general.
We help them, too! In fact, there are foods we eat that feed our microbiome. A diet high in fiber is essential since fiber is what transports food to our microbiome, thus helping it to help us stay healthy. Eating healthy foods with fiber keeps your microbiome healthy. Sadly, ultraprocessed foods (like fast or pre-packaged foods) do not have a firm matrix in their cell walls, which makes it more difficult for them to transport food you eat to feed your important microbiome. (Greger: How Not To Age) Most birthing parents and even birth professionals are unaware of the very important significance of our microbiome.
Challenging Beliefs: Is a Baby in the Womb Sterile Before Birth?
In the Womb
It has long been assumed that the human fetus is sterile. If this is true, it would mean that babies in the womb do not encounter any microbes until the moment of birth. In the past, there were opposing views between perinatal and microbiological researchers as to whether or not the human microbiome was seeded before birth. Some believed that research showing microbial communities (in the placenta, amniotic fluid, or meconium) were related to underlying contamination issues (in the sampling process itself).
However—new research and more modern techniques (that allow for more sensitive and accurate profiling of low-biomass samples) have found that meconium sampled does contain bacterial DNA. This points to evidence that the human fetus is exposed to bacteria before birth! This means that the baby in the womb is not sterile.
In Birth
All experts agree, however, that the major seeding of the microbiome—from the mother to the baby—occurs during vaginal birth. This happens in natural birth when the baby passes through the birth canal, close to the mother’s rectum. Near crowning, as the baby rotates and turns, their mouth and nose come in contact with their mother’s vaginal and rectal contents, where the baby receives a mouthful of the mother’s microbes. Because babies who pass through their mother’s vaginas appear to receive the most significant dose of her microbiome, providing a strengthened immune system, it is important not to resort to cesarean births unless medically necessary.
This is important because we want the baby to have a strong immune system. Without this major seeding, the baby’s immune system is compromised and subjected to the risks of asthma, allergies, obesity, and Type 1 diabetes. After birth (no matter the type), a baby can also receive more beneficial bacteria to build a healthier microbiome during breastfeeding.
Research through the years reveals more and more the understanding that babies already have bacteria and fungi in their guts during pregnancy. This process of colonization is believed to be a natural and steady one in the fetus and prepares the baby for life in the outside world. The field of study is still unfolding to answer, “What is the exact process for this seeding of the baby’s microbiome before birth?”
Benefits of microbiome seeding
In pregnancy
We are learning that the human body works via systems of networks that are interconnected. Robynne Chutkan, MD, in her book The Microbiome Solution, states that “During pregnancy, one of the most dramatic changes happens in a mother’s vagina… cells in the vaginal lining ramp up production of a carbohydrate called glycogen, sending glycogen-loving Lactobacillus bacteria into a feeding frenzy and increasing their numbers. Lactobacilli convert lactose and other sugars to lactic acid, creating an acidic, unfriendly environment that helps to protect the growing fetus from potential invaders.” (Chutkan 2015)
At birth
She goes on to say, “This brief act of swallowing a mouthful of our mother’s microbes as we enter the world confers unbelievably important benefits.” This is true because without the mother’s microbiome, the baby’s immune system is weaker than it would be otherwise (e.g. if a cesarean birth), so less able to fight off diseases. It turns out that exposure to bacteria is a critical early step in the development of our immune system.
After birth
The beneficial microbes contain special sugars—that are passed on when mothers breastfeed their babies—whose basic components are lactobacillus and other probiotics. These continue to help the baby differentiate between friend and foe bacteria. Therefore, a baby’s healthiest microbiome depends on being fed human milk. This is still another reason their mother’s breast milk is best for the optimal health and growth of a newborn.
Birthing parents want their babies to have an optimal start in life. Harman and Wakeford state in their book Your Baby’s Microbiome, “Receiving these microbes helps keep a baby’s organs functioning and protects him from disease. In return, the human body gives the microbes a home, and we provide them with food as the gut microbes help break down nutrients. This is a symbiotic process.” (Harman, 2017)
What role does the microbiome play in utero before birth, during birth, and after? These are fascinating questions we need to continue to learn more about. The body is always working to give us the best it can for our health. This goes to the BirthWorks Philosophy based on human values, including trust. Trusting mothers’ bodies and the birth process is essential to health.
The study of our microbiome continues to evolve in a way that is fascinating and helps us respect its importance. On September 20, 2025, Toni Harman and Alex Wakeford are conducting a worldwide premiere of their new film “The Microbirth Plan.” To view the trailer, visit http://microbirthplan.com/
