Microbiome Seeding: How Mom Shapes Baby’s Health from Birth

Nurture Genomics

September 2024

Welcoming your baby into the world and giving them the best start in life is everything to parents. That’s why we’re excited to introduce you to Tiny Health, a company dedicated to supporting families with microbiome testing. Founded by a mom for moms, Tiny Health is the first gut health test designed for mothers and babies under three years old.

Gut imbalances impact everything from immune development to the risk of conditions like asthma and allergies. So, finding and addressing imbalances early, in the first 1000 days, is critical to your baby’s lifelong health.

In this guest blog, the Tiny Health team delves into how beneficial microbes are transferred from mom to baby, beginning at birth. These microbes colonize the baby’s entire body, from their mouth and skin to their digestive tract, setting the foundation for their health.^1,2

Your baby’s first inheritance: microbes

You may have your mother’s smile or brown eyes, but she also gave you your first microbes.^3-5 Unlike genes, which we inherit at conception, the sharing of microbes between mom and baby continues after birth. During delivery, a mother passes on her gut, vaginal, and skin microbes to her baby. It’s essential for helping establish a healthy gut.

After birth, a mom continues to pass along friendly and beneficial microbes by breastfeeding and skin-to-skin contact. Through bonding, fathers, siblings, and caretakers also contribute beneficial microbes to the baby’s microbiome.

Many of these shared microbes are crucial in keeping your baby protected. The sooner they take hold, the sooner they begin teaching your newborn’s immune system how to develop. Your baby’s first microbes shape their long-term health.

The microbes that first seed your baby’s gut are influenced by several factors, including:

How you gave birth
Medical procedures during birth
Use of antibiotics and other medications

No matter the circumstances, a baby’s first 1,000 days is the optimal time to seed good bacteria and minimize the chances of unfriendly microbes taking hold.

Benefits of a vaginal birth

How you give birth shapes the composition of your baby’s gut microbiome in the first month of life and up to one year old. The links between birth mode—vaginal or C-section—and the baby’s gut microbiome are dramatic.^3,6,7 During a vaginal delivery, your baby touches both your vaginal and fecal microbes because the birth canal and rectum are close together.

Babies born vaginally have more beneficial species of Bifidobacterium, Bacteroides, and Parabacteroides than babies born by C-section.⁷

Bifidobacteria are friendly bacteria associated with good health because they:

Make lactate and short-chain fatty acids (SCFAs) when they digest breastmilk sugars called HMOs (human milk oligosaccharides), which makes it hard for unfriendly gut bacteria to survive.⁸
Play an essential role in training your baby’s immune system.^9-12
Support the growth of other bifidobacteria, which promotes a healthy microbiome.^9-13
Provide essential micronutrients, such as vitamins B6, B12, folate, and K.¹⁴

Like Bifidobacterium, Bacteroides and Parabacteroides also play a significant role in the early gut microbiome. These bacteria help to train the baby’s immune system and digest the starches when solids are introduced into your baby’s diet.

Having these friendly bacteria in the gut gives your baby the best opportunity for optimal microbiome development.

Impact of C-sections on seeding at birth

The World Health Organization suggests that C-section birth is only medically necessary in 10-15% of pregnancies, but they’re becoming more widespread globally. In the United States, 34% of babies are born by C-section.

Babies born via C-section don’t inherit the rich blend of beneficial microbes that come from a vaginal birth. And these microbes may help protect against chronic conditions such as asthma and allergies.^{3, 15-18}

By contrast, they get their mom’s skin bacteria and other less-friendly bacteria often found in hospitals, like Enterococcus, Klebsiella, and Clostridium.^3,17,19 Many of these bacteria carry antibiotic-resistant genes, making them challenging to eliminate.^20,21 This can be especially risky for premature babies.²² The unique microbiome signature from a C-section birth can last up to 4 years in children.³

Babies born by C-section have an increased risk of health issues like:

Asthma, allergic rhinitis, and eczema²⁰
Type 1 diabetes²³
Obesity²⁴
Gut-related conditions (e.g., celiac disease, food allergies)²⁵

More research is needed, but the evidence suggests that C-sections affect the microbial seeding of the baby’s gut. They should be carefully considered, and steps should be taken afterward to help restore the natural balance of your baby’s microbiome.

Medical treatments that may impact your baby’s microbiome

During labor and birth, your doctor or midwife may suggest painkillers or special instruments like forceps to help deliver your baby. Knowing your options before birth is helpful. We’ve compiled a list of hospital interventions they may offer you and their possible impact on your baby’s microbiome.

Epidurals are popular for pain relief, but they may interfere with the baby’s spontaneous breastfeeding behaviors in the first 24 hours.²⁶ Studies suggest it may be proportional to the amount of epidural received, although research on this topic is controversial.²⁷

We also know that procedures to induce labor (e.g., Pitocin) may increase the risk of C-section births compared to those that begin spontaneously.²⁸

Also, before or during labor, antibiotics can affect how a mother’s microbiome is passed to her baby.⁷ They are linked to lower levels of beneficial bacteria like Bifidobacterium and Bacteroides in babies and can lead to the growth of antibiotic-resistant bacteria in both moms and babies.

Women who have C-sections are 5 to 20 times more likely to get an infection than those who give birth vaginally, so antibiotics are typically given before C-section surgery to prevent infections.²⁹

The impact of interventions during labor on the mom and baby’s microbiome is not well studied. But we know that almost any medication given during birth, including epidurals and antibiotics, has the potential to reach your baby. When possible, opt for fewer interventions.

If you had or will have to take antibiotics before or during labor, check out our tips below on restoring your baby’s microbiome.

Five ways to help restore your baby’s microbiome after a C-section or antibiotics

Holding your baby skin-to-skin right after birth has many benefits. Babies stay warmer, cry less, and are more likely to breastfeed longer. If you can’t hold your baby, your partner can step in for you during that important skin-to-skin time.
Start breastfeeding as soon as possible. Breastmilk has many benefits—like helping your baby’s gut bacteria grow strong.
Consider vaginal seeding. Before deciding on whether it’s a good option, test your vaginal microbiome.
If breastfeeding isn’t an option, think about giving your baby probiotics and using an HMO prebiotics formula.
Seeding continues throughout life, most intensely in the first two years of your baby’s life. Playing outdoors, having pets, and exposure to natural environments have all been linked to reduced rates of allergies, asthma, and eczema in kids.

From breastfeeding to minimizing medical interventions to exploring practices like vaginal seeding, your baby’s health starts with you. Tiny Health is extending a $20 discount to all Nurture families. Enter code NURTURE during checkout to save on Baseline Assessments, Tiny+ Memberships, and Tiny+ Targeted programs. You are not alone in your journey to give your baby the best start possible.

1 C. Milani et al., “Exploring Vertical Transmission of Bifidobacteria from Mother to Child,” Appl Environ Microb, vol. 81, no. 20, pp. 7078–7087, 2015, doi: 10.1128/aem.02037-15.

2 P. Ferretti et al., “Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome,” Cell Host Microbe, vol. 24, no. 1, pp. 133-145.e5, 2018, doi: 10.1016/j.chom.2018.06.005.

3 J. Roswall et al., “Developmental trajectory of the healthy human gut microbiota during the first 5 years of life,” Cell Host Microbe, vol. 29, no. 5, pp. 765-776.e3, 2021, doi: 10.1016/j.chom.2021.02.021.

4 K. Korpela et al., “Selective maternal seeding and environment shape the human gut microbiome,” Genome Res, vol. 28, no. 4, pp. 561–568, 2018, doi: 10.1101/gr.233940.117.

5 C. Milani et al., “The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota,” Microbiol Mol Biol R, vol. 81, no. 4, pp. e00036-17, 2017, doi: 10.1128/mmbr.00036-17.

6 M. G. Dominguez-Bello et al., “Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns,” Proc National Acad Sci, vol. 107, no. 26, pp. 11971–11975, 2010, doi: 10.1073/pnas.1002601107.

7 Y. Shao et al., “Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,” Nature, vol. 574, no. 7776, pp. 117–121, 2019, doi: 10.1038/s41586-019-1560-1.

8 S. Fukuda et al., “Bifidobacteria can protect from enteropathogenic infection through production of acetate,” Nature, vol. 469, no. 7331, pp. 543–547, 2011, doi: 10.1038/nature09646.

9 I. O’Neill, Z. Schofield, and L. J. Hall, “Exploring the role of the microbiota member Bifidobacterium in modulating immune-linked diseases,” Emerg Top Life Sci, vol. 1, no. 4, pp. 333–349, 2017, doi: 10.1042/etls20170058.

10 B. M. Henrick et al., “Bifidobacteria-mediated immune system imprinting early in life,” Cell, 2021, doi: 10.1016/j.cell.2021.05.030.

11 B. M. Henrick et al., “Colonization by B. infantis EVC001 modulates enteric inflammation in exclusively breastfed infants,” Pediatr Res, vol. 86, no. 6, pp. 749–757, 2019, doi: 10.1038/s41390-019-0533-2.

12 J. E. Spreckels and A. Zhernakova, “Milk and bugs educate infant immune systems,” Immunity, vol. 54, no. 8, pp. 1633–1635, 2021, doi: 10.1016/j.immuni.2021.07.013.

13 S. A. Frese et al., “Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants,” Msphere, vol. 2, no. 6, pp. e00501-17, 2017, doi: 10.1128/msphere.00501-17.

14 C. M. Dieterich, J. P. Felice, E. O’Sullivan, and K. M. Rasmussen, “Breastfeeding and Health Outcomes for the Mother-Infant Dyad,” Pediatr Clin N Am, vol. 60, no. 1, pp. 31–48, 2013, doi: 10.1016/j.pcl.2012.09.010.

15 L. Wampach et al., “Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential,” Nat Commun, vol. 9, no. 1, p. 5091, 2018, doi: 10.1038/s41467-018-07631-x.

16 J. Stokholm et al., “Cesarean section changes neonatal gut colonization,” J Allergy Clin Immun, vol. 138, no. 3, pp. 881-889.e2, 2016, doi: 10.1016/j.jaci.2016.01.028.

17 F. Bäckhed et al., “Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life,” Cell Host Microbe, vol. 17, no. 5, pp. 690–703, 2015, doi: 10.1016/j.chom.2015.04.004.

18 N. A. Bokulich et al., “Antibiotics, birth mode, and diet shape microbiome maturation during early life,” Sci Transl Med, vol. 8, no. 343, pp. 343ra82-343ra82, 2016, doi: 10.1126/scitranslmed.aad7121.

19 T. Vatanen et al., “The human gut microbiome in early-onset type 1 diabetes from the TEDDY study,” Nature, vol. 562, no. 7728, pp. 589–594, 2018, doi: 10.1038/s41586-018-0620-2.

20 R. M. Lebeaux et al., “The infant gut resistome is associated with E. coli and early-life exposures,” Bmc Microbiol, vol. 21, no. 1, p. 201, 2021, doi: 10.1186/s12866-021-02129-x.

21 A. J. Gasparrini et al., “Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome,” Nat Microbiol, vol. 4, no. 12, pp. 2285–2297, 2019, doi: 10.1038/s41564-019-0550-2.

22 C. J. Hill et al., “Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort,” Microbiome, vol. 5, no. 1, p. 4, 2017, doi: 10.1186/s40168-016-0213-y.

23 C. S. Algert, A. McElduff, J. M. Morris, and C. L. Roberts, “Perinatal risk factors for early onset of Type 1 diabetes in a 2000–2005 birth cohort,” Diabetic Med, vol. 26, no. 12, pp. 1193–1197, 2009, doi: 10.1111/j.1464-5491.2009.02878.x.

24 S. Y. Huh et al., “Delivery by caesarean section and risk of obesity in preschool age children: a prospective cohort study,” Arch Dis Child, vol. 97, no. 7, p. 610, 2012, doi: 10.1136/archdischild-2011-301141.

25 E. Decker, M. Hornef, and S. Stockinger, “Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children,” Gut Microbes, vol. 2, no. 2, pp. 91–98, 2011, doi: 10.4161/gmic.2.2.15414.

26 A. Ransjö‐Arvidson, A. Matthiesen, G. Lilja, E. Nissen, A. Widström, and K. Uvnäs‐Moberg, “Maternal Analgesia During Labor Disturbs Newborn Behavior: Effects on Breastfeeding, Temperature, and Crying,” Birth, vol. 28, no. 1, pp. 5–12, 2001, doi: 10.1046/j.1523-536x.2001.00005.x.

27 J. N. Lind, C. G. Perrine, and R. Li, “Relationship between Use of Labor Pain Medications and Delayed Onset of Lactation,” J Hum Lact, vol. 30, no. 2, pp. 167–173, 2013, doi: 10.1177/0890334413520189.

28 M.-A. Davey and J. King, “Caesarean section following induction of labour in uncomplicated first births- a population-based cross-sectional analysis of 42,950 births,” Bmc Pregnancy Childb, vol. 16, no. 1, p. 92, 2016, doi: 10.1186/s12884-016-0869-0.

29 K. Conroy, A. F. Koenig, Y.-H. Yu, A. Courtney, H. J. Lee, and E. R. Norwitz, “Infectious morbidity after cesarean delivery: 10 strategies to reduce risk.,” Rev Obstetrics Gynecol, vol. 5, no. 2, pp. 69–77, 2012.

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