What Pregnant Women Need to Know About the Inner Ecosystem

Over one hundred years ago, a French pediatrician named Henry Tissier established that infants develop in a sterile environment. This means no bacteria, no viruses, and no yeast are in the womb with a developing baby. And any microbe found in the uterus is a dangerous threat to the health of the baby.

Prenatal microbes might shape a lifetime of health.

But in a recent paper, researchers at Vanderbilt University in Nashville, Tennessee, challenge that dogma. They assert that—like the rest of the human body—the womb is not sterile. (1)

Mounting evidence suggests that a growing baby acquires microbes before birth.

Microbes contribute to 99% of all genetic information in the body, so a disruption of this process can “mutate” the inner ecosystem. So far, we know that these mutations may contribute to the progression of obesity, heart disease, autoimmune disease, allergies, mood disorders, hormonal imbalances, and dementia. Indeed, prenatal microbes might shape a lifetime of health.

Baby’s First Stool Is Not Sterile

Researchers have discovered that babies are exposed to microbes in the womb. A mother that consumes beneficial bacteria can influence her baby’s health before birth.

Most of the medical community believes that the womb is a sterile environment because the placenta acts as barrier, keeping a growing baby safe from infection.

But very few studies have looked at the inner ecosystem of the uterus—if there is one—during a healthy pregnancy.

Those that have found:

  • Bacteria in umbilical cord blood (2)
  • Bacteria in amniotic fluid, the protective liquid that surrounds a developing baby (3)(4)
  • Bacteria in fetal membranes, the sacs that surround a baby as it grows (5)

These findings imply that healthy babies are exposed to bacteria in utero. And that the womb is not a sterile environment. (6) In fact, while most physicians and scientists believe that the intestinal tract of a newborn is a “blank canvas,” the latest research tells us that this is far from accurate.

To learn more about the prenatal inner ecosystem, researchers at University Complutense in Madrid, Spain, asked the question: “Is baby’s first stool sterile?” (7)

The first stool of a baby is called meconium. While developing in the womb, babies ingest amniotic fluid. Meconium, which is generally thick and tarry, is the result of time spent in the womb.

Meconium is not sterile, as previously assumed. Baby’s first stool is home to a complex community of microbes. And animal studies show that these microbes are passed down from mother to child.

Researchers in Madrid fed pregnant mice specific strains of gut bacteria. They then examined the first stool of baby mice that had been born via sterile C-section.

They found that:

  • Their meconium contained the same microbes that had been given to their mothers as a probiotic.
  • Those mothers that did not receive the probiotic did not have babies with meconium that contained this specific strain of bacteria.
  • The inner ecosystem of a newborn’s gut is less complex than an adult’s; nonetheless, there is still evidence that it is there.

How a Mother Passes on Her Microbial Heritage

While a newborn may begin life with a prenatal inner ecosystem, there are other ways that a mother passes along her own microbial blueprint. For example, we know that factors such as birth route and first nourishment shape a baby’s inner ecosystem.

As a newborn passes through a mother’s birth canal, it is “smeared” with microbes. (8) These microbes colonize the skin, mouth, nose, and gut of the newborn. Whereas babies that are born via C-section are colonized with microbes that are similar to those found on the skin. (9)

Studies show that Cesarean delivery can influence the long-term health of a child, especially when it comes to disorders that involve the immune system.

For example, babies born via C-section are more likely to develop:

  • Allergic rhinitis
  • Asthma (10)
  • Celiac disease (11)
  • Type 1 diabetes (12)
  • Inflammatory bowel disease (13)

Research also shows that the microbes belonging to a baby born via C-section are no more related to the microbes belonging to the mother than those of a stranger. This means that C-section babies pick up microbes from those who handle the newborn baby—breaking the microbial blueprint that is passed down from mother to child.

Breastfeeding is another way that a mother passes her inner ecology to her infant.

Studies show that breast milk helps to:

  • Fortify the immune system (14)
  • Safeguard against infection (15)
  • Protect against the development of allergies and asthma (16)

Your Baby’s Prenatal Ecosystem Matters

There’s no denying it. The inner ecosystem of microbes living in your digestive tract plays a major role in overall health.

Though too small to be seen with the naked eye, microbial cells outnumber your own cells 10 to 1. Each human being harbors upward of 100 trillion microbial cells, which contribute over 8 million genes to our own set of 22,000. (17)(18)

While the inner ecosystem affects every aspect of health, scientific studies have confirmed that interactions between the human body and the inner ecosystem influence:

  • Gut development
  • Digestion
  • Immune system development
  • Dental health
  • Resistance to infection
  • Metabolism

The development of a baby’s immune system and gastrointestinal tract rely on the interaction that occurs between the body and the microbes that inhabit it. This includes microbes acquired before birth.

Because we begin building our inner ecosystem while in the womb, mothers-to-be can focus on eating fermented vegetables and drinking coconut water kefir for the best form of living beneficial bacteria to colonize the gut and boost the immune system.

Even more, it’s essential to begin rebuilding your inner ecosystem before pregnancy to ensure that your child has the best start possible.

What To Remember Most About This Article:

The womb was once thought to be a sterile environment, but modern researchers disagree. Research supports that a growing baby in the womb will acquire microbes before birth. Microbes make up the inner ecosystem, and a disruption in this process can contribute to health issues like allergies, heart disease, autoimmune disease, and obesity.

A mother passes her microbial blueprint along to her baby throughout pregnancy and during birth. A newborn is covered with microbes when moving through the birth canal; studies support that a C-section delivery can influence the long-term health of a baby, especially related to immunity.

A mother also shares her inner ecology with her baby through breastfeeding to boost the immune system, protect against infection, and reduce the risk of allergies and asthma. The health of the inner ecosystem is pivotal for gut and immune system development, infection resistance, metabolism, and dental health.

If you are pregnant or trying to conceive, now is the perfect time to support your inner ecosystem with fermented vegetables and coconut water kefir. Friendly bacteria will colonize your baby’s gut before birth to strengthen immunity and overall health.

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  1. Funkhouser, L. J., & Bordenstein, S. R. (2013). Mom Knows Best: The Universality of Maternal Microbial Transmission. PLoS biology, 11(8), e1001631.
  2. Jimenez E, Fernandez L, Marin ML, Martin R, Odriozola JM, et al. (2005) Isolation of commensal bacteria from umbilical cord blood of healthy neonates born by cesarean section. Curr Microbiol 51: 270–274.
  3. Bearfield C, Davenport ES, Sivapathasundaram V, Allaker RP (2002) Possible association between amniotic fluid micro-organism infection and microflora in the mouth. BJOG 109: 527–533.
  4. Rautava S, Collado MC, Salminen S, Isolauri E (2012) Probiotics modulate host-microbe interaction in the placenta and fetal gut: a randomized, double-blind, placebo-controlled trial. Neonatology 102: 178–184.
  5. Steel JH, Malatos S, Kennea N, Edwards AD, Miles L, et al. (2005) Bacteria and inflammatory cells in fetal membranes do not always cause preterm labor. Pediatr Res 57: 404–411.
  6. Madan, J. C., Farzan, S. F., Hibberd, P. L., & Karagas, M. R. (2012). Normal neonatal microbiome variation in relation to environmental factors, infection and allergy. Current opinion in pediatrics, 24(6), 753-759.
  7. Jimenez E, Marin ML, Martin R, Odriozola JM, Olivares M, et al. (2008) Is meconium from healthy newborns actually sterile? Res Microbiol 159: 187–193.
  8. Huh SY, Rifas-Shiman SL, Zera CA, Edwards JW, Oken E, et al. (2012) Delivery by caesarean section and risk of obesity in preschool age children: a prospective cohort study. Arch Dis Child 97: 610–616.
  9. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, et al. (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 107: 11971–11975.
  10. Renz-Polster H, David MR, Buist AS, Vollmer WM, O’Connor EA, et al. (2005) Caesarean section delivery and the risk of allergic disorders in childhood. Clin Exp Allergy 35: 1466–1472.
  11. Decker E, Engelmann G, Findeisen A, Gerner P, Laass M, et al. (2010) Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children. Pediatrics 125: e1433–1440.
  12. Cardwell CR, Stene LC, Joner G, Cinek O, Svensson J, et al. (2008) Caesarean section is associated with an increased risk of childhood-onset type 1 diabetes mellitus: a meta-analysis of observational studies. Diabetologia 51: 726–735.
  13. Bager P, Simonsen J, Nielsen NM, Frisch M (2012) Cesarean section and offspring’s risk of inflammatory bowel disease: a national cohort study. Inflamm Bowel Dis 18: 857–862.
  14. Diaz-Ropero MP, Martin R, Sierra S, Lara-Villoslada F, Rodriguez JM, et al. (2007) Two Lactobacillus strains, isolated from breast milk, differently modulate the immune response. J Appl Microbiol 102: 337–343.
  15. Maldonado J, Canabate F, Sempere L, Vela F, Sanchez AR, et al. (2012) Human milk probiotic Lactobacillus fermentum CECT5716 reduces the incidence of gastrointestinal and upper respiratory tract infections in infants. J Pediatr Gastroenterol Nutr 54: 55–61.
  16. Fernandez L, Langa S, Martin V, Maldonado A, Jimenez E, et al. (2013) The human milk microbiota: origin and potential roles in health and disease. Pharmacol Res 69: 1–10.
  17. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95: 6578–6583.
  18. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355–1359.
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