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By Cathy Daub founder and president of BWI and Horatio Daub, MD

I want to share with you the excitement I felt in learning more about the microbiome at the recent Microbirth Plan Virtual Conference held April 29-30, 2023 by Toni Harman and Alex Wakeford of Alto Films based in England.  

Our Microbiome

The microbiome is a collection of microorganisms and their genes living in a particular environment. In fact, we are mainly microbes because our genes and even the majority of cells in our body are microbial. Overall, the speakers addressed the belief that we have seen ourselves as if we are only humans, ignoring the important role our microbiome plays in our well-being and health.  

Our earth is a microbial planet and we are a reflection of life on earth.  In fact, microbes are the predominant lifeform on Earth.  We have more microbial cells in our bodies than human cells and together they form a symbiotic relationship with each other.  This requires a new understanding of our identity. All humans need to thrive and adapt in this microbiome world. 


Most of these microbes are good, but others are pathogenic and promote disease.  Dysbiosis occurs when there is an imbalance within a superorganism i.e. the wrong microbes in the wrong location which has the potential for disease.  For example, our immune system requires organ and tissue interactions with specific microbes at precise times especially at the time of birth.

When the infant microbiome is disrupted by exposure to microbes other than those we have evolved with, their immune system can be incorrectly primed leading to inappropriate immune responses as beneficial microbes are not correctly recognized so the immune system destroys them. Conversely, harmful microbes may not be identified as a threat, allowing disease. 

Global  Effects of Our Microbiome

The enormity of this new way of understanding ourselves is knowing that it is our microbiome that affects system biology such as sleep (which has been described as the epicenter of most chronic disease), our circadian clocks, and inflammation which is usually the precursor to disease and aging.   Our microbiome has short and long-term global effects on our health affecting our immune system and even telomere lengths. 

Sacred Bond Between Microbiome and Immunity: Effects of Microbiome on Newborn Babies

Having an understanding of our microbiome is important for everyone but especially for newborn babies at the moment of birth.  There is a biologically sacred bond that exists between the baby’s microbiome and its immune system and other vital systems.   Early life was seen by the speakers as a critical period for our health from the moment of birth and into the first few years of life and even having an impact on our longevity and healthy lifespan.    Everyone needs to know that there is a critical window of vulnerability that exists for the developmental programming of the microbiome that determines vulnerability to disease.

Major Seeding of Microbiome for Babies

Over thousands of years, babies have been born passing near their mother’s rectum.  This is where they receive the major seeding of their mother’s microbiome – just this brief act is a precious gift for now the newborn’s immune system is better protected against other germs as it is able to differentiate friend from foe bacteria. This is the reason that babies need nurtured microbiota to face the world.  

The depletion or destruction of the microbiome is known to propagate predictable interconnected diseases such as asthma, allergies, obesity, Type 1 diabetes, and other autoimmune diseases.  It is known that the asthma child and obese children are prone to many other diseases into adult life.  Babies who do not receive this major seeding – who do not pass through the vagina as in a cesarean birth, are more prone to these diseases. The newborn needs to receive the “good” bacteria to protect his health by fighting off the “unfriendly” bacteria.  Attempts to give cesarean babies oral and skin “swabs” of their mother’s microbiome has not yet been approved due to risk of infection and more studies are needed to see if the benefits exceed the risks. 

Microbiome and Breastmilk

Nature continues to try to protect us through human breastfeeding as breastmilk contributes additional microbes.  This is the reason breastfeeding is considered the gold standard and it is especially important for women having a cesarean.  However, the major seeding, the most protective, is what the baby receives passing through the vagina for birth. The consequence for a baby born by cesarean and who is also not breastfeeding has a double negative impact on his immune system. 

Furthermore, when the baby doesn’t receive human milk, inflammation is promoted, resulting in a loss of gut-lining integrity allowing allergens, pathogenic bacteria, and viruses to enter the blood stream more freely.  There is then a higher risk of short and long-term metabolic diseases, infections, and asthma.  

Disruptors of a Healthy Microbiome

As a society are we thinking about what disrupts our microbiome?  Antibiotics are major disruptors of our microbiome and should be used only if medically necessary.  Other disruptors are additives in foods, emulsifiers, heavy metals and other chemicals. 

Our microbiome is located in the orifices - points of entry into our bodies. We are breathimg them in via our respiratory system, eating them in our food, drinking them in water and absorbing them through our skin.  Thus, our microbiome is usually the first to encounter pathogens or toxins.  How robust and healthy our microbiome and therefore our immune system is, has an impact on whether or not we are vulnerable or protected from microbial pathogens and toxins.

Exposure to Animals

A diversity of microbiome is protective and a natural way to keep us healthy.  Being around animals, especially dogs was described as beneficial to creating healthy diversity in our microbiome.   Other ways are encouraging parents to take their children to local petting zoos and allowing them to play in nature’s dirt to increase this diversity. 

Food and our Microbiome

Our gut has been called “the second brain” because it has more microbes than the brain.  That makes the food we eat especially important.  One speaker described leafy greens and foods with lots of fiber as the best foods for our microbiome. In fact, nitrates from leafy greens break down in the mouth to nitric acid whose function is to dilate blood vessels. This dilation improves blood flow thus lowering blood pressure thereby preventing high blood pressure, the most common risk factor for heart disease.  But, using things like mouthwash or brushing the tongue disrupts this natural process so that our bodies don’t receive the major advantage the leafy greens would give us.

Protecting a Baby’s Microbiome at Birth

In the womb the fetus is sterile so at birth there is a race for the germs.  Whose germs do you want your baby to have?  Yours? Or those of your birth team?  Or the hospital or home environment? 

What can we do at birth to help protect the baby’s microbiome?  A midwife speaker suggested:

  • Minimize physical or close contact with babies except for the mother and family members, can reduce exposure to harmful hospital microbes common in a hospital environment.  
  • Reduce the number of vaginal exams in labor. 
  • Avoid touching and breathing over babies. 
  • Avoid lithotomy and semi-sitting positions. 
  • Avoid forced pushing. 
  • Use perineal warm compresses to decrease perineal tears.  
  • Keep the sacrum free to move. 
  • Be upright and active in labor and birth.
  • Have a calm environment. 
  • Use floor mats so women can assume hands and knees positions.
  • Wear masks to reduce babies’ exposure to our microbes.
  • Catch babies in a sheet that has the mother’s microbes on it.
  • Wear sterile gloves and gowns when handling babies.
  • Support skin-to-skin contact between parents and baby to replenish skin microbes.
  • Encourage breastfeeding.
  • Have zero separation of mother and baby in the first days after birth. 


Microbiome depletion and the resulting epidemic can be caused by overuse of antibiotics, increases in cesarean section and decreased duration of breastfeeding that we are seeing in the USA today.  In addition, various food additives, drugs and chemicals added to foods affect our microbiome.  Urbanization is also a reason due to decreased contact with animals.  People who still live in their culturally distinct communities tend to be healthier.  Finally, hospital birth is associated with a risk of getting hospital associated microbes that are not good for a newborn baby.  

If you are working with birthing parents now, or are pregnant yourself and reading this, it is my hope that you will envision your body in a unique way, that of a microbiome system that needs to stay in balance to offer you the best health for many years.  It is also my hope that you will share information about the microbiome with others and encourage them to watch the film “Microbirth” by Toni Harman and Alex Wakeford. 

To watch Microbirth – you can rent/download from Vimeo on demand:

Or you can watch Microbirth at