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Healthy Gut, Healthy Baby! Microbiome basics

The 6 Seed and Feed events that optimize baby’s gut microbiome

1. When the waters break, microbes from the vagina can now reach the

fetus. Beneficial microbes in the vagina have multiplied in the third

trimester in preparation for this! Remember, vaginal exams at this stage

allow microbes from the health care provider’s gloved hands to also

reach the fetus. Ugh!

2. Passage through the vagina where the baby picks up beneficial

microbes especially lactobacilli – one of the good ones.

3. Baby’s contact with the birthing person’s perineum colonizes the baby

with their parents’ gut microbes – yes, I’m talking about poop!

4. Baby is now breathing in their first breaths and millions of microbes.

From a microbial perspective, do you think the most beneficial microbes

for baby would be from the Operating room, a labor and delivery room,

a birthing center room or the baby’s home environment? Answer: baby’s

microbiome will be optimized by them breathing the air from their

family’s home environment.

5. Skin to Skin contact with the birthing person or the non birthing partner

if this is not possible. One of the many benefits of skin to skin is that it

supports a healthy microbiome and colonizes the baby’s skin, mouth,

nose the right kind of beneficial microbes from the birther’s vagina and

gut from their feces and then from the environment. Breastfeeding

feeds the right kind of beneficial microbes from their parents.

6. Now all these beneficial microbes that the baby has acquired during

birth need to be fed. How? With Human Milk Oligosaccharides, also

known as HMO’s. HMO’s are unique to mammalian milk and there are

200 different types of HMO”s in human milk! HMO’s are indigestible in

the baby’s gut! So what’s so great about them? They feed the

beneficial microbes in the baby’s gut such as bifidobacterial. These

beneficial microbes are able to break down the bonds of HMO’s and

access the HMO sugars. By feeding these beneficial microbes, the

infant’s immune system is optimally trained to learn immune tolerance.

(recognize the difference between what is beneficial and what is


Cesarean birth, formula feeding, and antibiotics all affect the healthy

colonization of the infant gut. The good news is that the gut microbiome of

cesarean born babies who are exclusively fed breast milk starts to closely

resemble the gut microbiome of vaginally born babies after about 6 months

of exclusive breastmilk.

A 2018 study by Stewart et al found that breast milk was the most

important factor in shaping the infant microbiome; more important than

maternal health, mode of birth, household siblings, pets, probiotics,


In my next blog on this topic, we’ll discuss how the naïve immune system of

the baby can be optimally trained.

If you would like to learn more about this important topic, I am offering an online mini-workshop on August 6 at 10am, and a full in-person class at Babymoon Inn in Phoenix on Saturday morning September 28, 2024.

Online mini-workshop: Register here

In-person class: Register at or email for more details.

Penny Bussell Stansfield, Microbirth Approved Provider.

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