A Microbiome is Born: Unique Tools for Baby and Mom

By: Carla Abate

When I became pregnant 13 years ago for the first time, I never would have imagined delivering by cesarean section. I had recently finished a hypnobirthing class and would have gladly birthed at home if my husband was on board. But after my water broke, my progress slowed and I was scolded by my obstetrician to “do what I should have done a long time ago,” prepare for a c-section. Thankfully, I did not spend much time mourning the birth experience I could not have, nor the poor bedside manner of my doctor. Instead, I decided to empower myself with the tools my baby and I would both need for a robust entry into the next phase of our lives.

So much attention is given these days to comparing health outcomes of cesarean-born babies to vaginally born babies, as well as breast-fed babies to formula-fed babies. More than any other period, the perinatal period appears to offer the most significant window of opportunity for modification of future disease risk. Why? Because of the trillions of microbes that coexist within us that we refer to as the microbiome.

The concerns with c-section delivery are twofold:

  1. First, it is largely accepted that much of the microbiome is picked up by way of passage through the birth canal.
  2. Second, c-section mothers are routinely administered antibiotics prior to surgery. These transfer to the baby, having a profoundly negative impact on the microbiome, often observed years later.

Together, these factors explain the correlation between c-section delivery and microbiome alterations associated with greater disease risk (Stinson, Payne, and Keelan, 2018). C-section delivery is associated with greater risk of:

  • allergies
  • obesity
  • immune disfunction
  • Other chronic disease


Worried that my baby did not receive a microbiome replete with the beneficial microbes central to the development of his little immune system, I began to explore the use of probiotics. Well aware of the relationship between antibiotics and probiotics, I knew that I, as well as my baby, would benefit from including these in our recovery toolbox. (Grazul, Kanda, and Gondek, 2016). Although antibiotics are passed through breastmilk, the benefits of breastfeeding often outweigh this risk. Not only was I passing along the probiotics through my milk, but numerous Human Milk Oligosaccharides (HMOs) commonly known as prebiotics, present in breastmilk, transfer to baby as well. These serve as a fuel source for the bacteria group Bifidobacteria infantis, recognized as one of the major players in early infant microbiome development. Today, more and more babies are being born devoid of this health-promoting bacteria, leading to what many researchers have termed Newborn Gut Deficiency.

Supplementation alone however is not nearly as effective as doing so while also making permanent dietary shifts that have an enduring influence on the microbiome. For example, eliminating refined sugars and processed foods starve the pathogenic strains of bacteria that preferentially feed on these types of foods; while fresh vegetables rich in fiber provide nourishment to the sorts of bacteria we benefit from. Just as nature intended!

Vaginal Seeding

Vaginal seeding is a procedure that involves swabbing the infant’s mouth with vaginal fluid with the assumption that the vaginal microbes will transfer and colonize in the baby. Proponents of this practice argue that it is relatively safe as long as the mother is screened for potential pathogens prior to implementation. A relatively small study backs up the use of this practice by finding similar microbiomes in c-section babies swabbed and babies born vaginally (Dominguez-Bello, De Jesus-Laboy, Shen, et al). C-section-born babies that weren’t swabbed did not display this similarity. However, there is still debate as to whether the microbes of the vaginal fluid are designed to colonize the gut at all. Critics of this technique argue that it is not the vaginal microbes that seed the infant’s gut, but those of the mother’s colon that are relevant.

Emergent vs. Scheduled C-section

Perhaps the most empowering emerging information is that even in the absence of vaginal birth, labor itself plays a role in the microbiome transfer from mom to baby. According to a 2019 survey published in the Journal of Pregnancy, 42% of c-sections are elective. However, researchers speculate that c-sections involving the onset of labor, in which the fetal membranes have ruptured, are exposed to vaginal bacteria that planned c-section babies elude. Research indicates a stronger link between elective c-section delivery and disorders such as celiac and asthma compared with emergency c-section (Stinson, Payne, and Keelan, 2018).

Today, I have two healthy boys both born via unplanned c-section. Both were breastfed and supplemented with probiotics. Neither have allergies to date at 12 and 9 years. As a nutrition therapist that focuses on the perinatal stages, I believe microbiome education is paramount.

How to support an optimal microbiome during the perinatal period:

  • Aim for natural birth-consult your doctor to determine when c-section is medically necessary
  • Consult your obstetrician or midwife about vaginal seeding
  • Obtain lactation education prior to birth if possible to support successful breastfeeding
  • Consult your physician about the introduction of probiotics in the final month of pregnancy through to the first few months postpartum. These can be taken by mom as well as placed on the nipple as a paste from powder form or put in formula when breast-feeding is unattainable
  • Avoid unnecessary antibiotic exposure-this includes in the animal products we consume-choose organic and grass-fed
  • Eat a diet rich in whole foods and prebiotic foods
  • Get outdoors and keep pets around-research indicates greater bacterial diversity with these exposures (Bloomfield, Rook, Scott, Shanahan, Stanwell-Smith, and Turner, 2016)


  1. Grazul H, Kanda LL, Gondek D. Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice. Gut Microbes. 2016;7(2):101-14. doi: 10.1080/19490976.2016.1138197. Epub 2016 Mar 10. PMID: 26963277; PMCID: PMC4856465.
  2. Stinson LF, Payne MS, Keelan JA. A Critical Review of the Bacterial Baptism Hypothesis and the Impact of Cesarean Delivery on the Infant Microbiome. Front Med (Lausanne). 2018;5:135. Published 2018 May 4. doi:10.3389/fmed.2018.00135
  3. Bloomfield SF, Rook GA, Scott EA, Shanahan F, Stanwell-Smith R, Turner P. Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene. Perspect Public Health. 2016;136(4):213-224. doi:10.1177/1757913916650225
  4. Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med. 2016;22(3):250-253. doi:10.1038/nm.4039


Carla Abate is a board certified NANP member, an advocate for the importance of nutrition during the perinatal stages, and a family wellness educator. A Certified Master Nutrition Therapist and Postpartum Doula, she is also a wife, and mother of two boys. Her experience with pregnancy and entering motherhood helped inspire her work today. Motherhood brought an abundance of self-growth, inspiration, and courage. It also brought great challenge and forced Carla to dive into her own wellness journey. 

Today, it’s Carla’s mission to help other mothers flourish throughout pregnancy and bring well-nourished, thriving bundles of joy into the world.

For more information visit www.rebelrootsnutrition.com or email Carla at carla@rebelrootsnutrition.com.

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