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Birth Establishes the Infant Microbiome

April 2017

Authors Toni Harman and Alex Wakeford remind us of two distinct events which occur at birth. The first is that all of us as parents have encountered… the joy of meeting your new baby face-to-face immediately after delivery. Just knowing that you have created and birthed a human life is often a lifelong memory. The second event, though, science is just learning more about… the beginning of the infant microbiome. “The seeding of the baby’s gut microbiome… could have lifelong health consequences… Other factors such as genetics, the mother’s health and diet, and the mode of infant feeding may also play their part in the establishment of the baby’s gut microbiome, but the latest research indicates that the way in which we are born could be critical,” (p 38).


Infant development takes place in a relatively sterile uterine environment; scientists have discovered small colonies of bacteria in the placenta, the amniotic fluid, and suspect there are some in the developing infant intestinal tract. These bacteria, detected in 2015, are suspected factors in preterm birth and further research may shed light into this process.

Here are just a few highlights of all the known factors in the infant developing a healthy gut microbiome:

  1. The mother’s oral bacteria change to be able to transfer healthy microbes to her baby.
  2. The vaginal flora change throughout the pregnancy, but produce a much higher level of lactobacilli (“friendly bacteria”) in the third trimester. Lactobacilli work to convert lactose and other sugars into lactic acid for energy.
  3. The vaginal pH become highly acidic due to the high level of lactobacilli, limiting the bacterial diversity and preventing bacterial entrance into the uterus, placenta, and baby.
  4. Vaginal deliveries often allow the birthing baby to come into contact with the mother’s intestinal microbes through fecal matter.
  5. Intestinal bacterial changes for the pregnant mother extend from the oral cavity to the rectum, all in preparation for higher energy needs for mother and creation of the perfect microbiome for the infant.
  6. Rupture of the amniotic sack provides the first seeding of the infant’s microbiome through the vaginal microbes, which the infant’s skin, eyes, nose and mouth quickly absorbs.
  7. Lactobacilli enter into the infant’s gut with swallowing, in preparation for the first breastfeeding following birth. These microbes inhibit competing and possibly dangerous bacteria from colonizing the infant’s gut. Think of this as nature’s first antibiotic!
  8. Lactobacilli also train the infant’s immune system, and I’ll go into more details on this topic in a separate post.
  9. Once delivered, the baby is suddenly bombarded with microbes from mother, father, physician, nurses, air, and more; these help lay the foundation for lifelong health and immunity.

Kathy Parkes, MSN-Ed, BSPsy, RN, IBCLC, RLC, FILCA

Professional Development Educator



Your Baby’s Microbiome: The Critical Role of Vaginal Birth and Breastfeeding For Lifelong Health. (2016). Toni Harman and Alex Wakeford. Chelsea Green Publishing. White River Junction, Vermont.

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