The Infant Gut Microbiome: How Birth and Feeding Practices May Influence Development

By Birth & Baby University · Last updated: October 2026 · 8 min read

The infant gut microbiome has become one of the most talked-about topics in perinatal health. Claims about cesarean birth “damaging” a baby’s microbes, about swabs that “restore” them, and about probiotics that “fix” them circulate widely among parents, and some come from the same researchers whose careful studies are more cautious than the headlines. Postpartum doulas are asked about all of it. The science is moving quickly and is still mostly descriptive: it shows that birth and feeding practices are associated with differences in which microbes colonize babies, but it has not yet shown that changing those differences improves a child’s health. This article summarizes what the main studies and professional statements show, what remains unproven, and how to talk about it responsibly.

Key takeaways

Quick answer: delivery mode, feeding, antibiotic exposure and the household all shape which microbes colonize an infant’s gut, and breastfeeding and birth mode are among the factors most strongly associated with microbiome structure in a large cohort. Whether those differences cause later health problems, or whether interventions such as vaginal seeding improve outcomes, is not established. ACOG advises that vaginal seeding not be performed outside approved research.

• A study that followed 25 mother-infant pairs found a rapid influx of microbes at birth followed by strong selection in the first days, with maternal skin and vaginal strains colonizing only transiently and maternal gut strains proving more persistent in the infant gut.
• In a cohort of 903 children, receipt of breast milk (exclusive or partial) was the most significant factor associated with the microbiome structure, and birth mode was also significantly associated during the first phase, with higher levels of Bacteroides in infants delivered vaginally.
• A systematic review of eight studies of vaginal seeding in cesarean-born infants (558 infants) concluded the evidence indicates modest changes in the gut microbiome and that further clinical studies are necessary to understand the effect on health outcomes.
• ACOG states that vaginal seeding should not be performed outside the context of an institutional review board-approved research protocol until adequate data on safety and benefit are available.

What the research says

How the first microbes arrive. Ferretti and colleagues’ 2018 study in Cell Host & Microbe sampled 25 mother-infant pairs across multiple body sites from birth to 4 months postpartum with strain-level metagenomics. They described a rapid influx of microbes at birth followed by strong selection during the first days of life, found that maternal skin and vaginal strains colonize only transiently and that infants continue to acquire microbes from distinct maternal sources after birth, and reported that maternal gut strains were more persistent in the infant gut and better adapted ecologically than those acquired from other sources. The sample is small, so the study shows a detailed picture of transmission pathways in a few pairs, not population rates. It also complicates the idea that a single event at birth sets the infant’s microbiome for life.

What shapes the microbiome over time. Stewart and colleagues’ TEDDY study (2018) analyzed stool samples from 903 children between 3 and 46 months of age. They described three phases of microbiome progression: a developmental phase (months 3 to 14), a transitional phase (months 15 to 30) and a stable phase (months 31 to 46). Receipt of breast milk, exclusive or partial, was the most significant factor associated with microbiome structure, and breastfeeding was associated with higher levels of Bifidobacterium species. Cessation of breast milk was followed by faster maturation of the gut microbiome. Birth mode was significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides, particularly Bacteroides fragilis, in vaginally delivered infants. Geographic location and household exposures such as siblings and pets were also important. The study was designed around type 1 diabetes research, so its children may not represent all children, and the analysis found only subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. This is an observational study in a high-risk cohort, so associations do not show that breastfeeding or birth mode causes any health outcome through the microbiome.

Vaginal seeding. Vaginal seeding means wiping a newborn’s mouth, nose or skin with a gauze or swab exposed to the mother’s vaginal fluids, with the aim of transferring vaginal microbes to cesarean-born babies. ACOG’s Committee Opinion 725 (2017) notes the theory that it might reduce subsequent risk of asthma, atopic disease and immune disorders, and concludes that it should not be performed outside the context of an institutional review board-approved research protocol until adequate data on safety and benefit become available. Since then, trials have appeared. In a double-blind, randomized, placebo-controlled trial of 20 elective, prelabor cesarean-born neonates, Mueller and colleagues (2023) found that vaginal seeding increased mother-to-neonate microbiota transmission and caused compositional changes, along with a reduction in alpha diversity of the skin and stool microbiota. The authors say larger randomized studies are needed. A 2024 systematic review by Wang and colleagues of eight experimental studies (274 seeded and 284 non-seeded cesarean-born infants and 261 vaginally born infants) reported that seeding may increase the relative abundance of Bacteroides and Lactobacillus, that results on microbial diversity conflict, and that current evidence indicates modest changes in the gut microbiome, with further clinical studies needed to understand health outcomes and risks. None of the abstracts read reported a clinical benefit. A later ACOG update was not searched for, so check whether one exists.

What this means for doulas

• Keep the message balanced. Birth mode and feeding are associated with differences in gut microbes. That does not mean that a cesarean birth or formula feeding harms a child’s health, and it should never become a source of guilt.
• Do not recommend vaginal seeding. ACOG’s position is that it should only occur within approved research. If a parent asks, say so and refer to the obstetric provider.
• Do not recommend probiotics for babies. None of the sources reviewed established infant probiotic use, and products and doses are a clinical decision.
• Support what is well supported. Breastfeeding is recommended for many reasons beyond the microbiome (see The First Hour After Birth: Why Early Feeding Support Matters),.
• Be careful with product marketing. Microbiome tests and supplements for babies are heavily advertised, and no reviewed evidence shows that testing a baby’s stool microbiome guides care.

Putting the evidence into practice

1. Listen to the worry. Many parents ask because of a cesarean birth or antibiotics during labor, and feel guilty. Acknowledge the feeling before the facts.
2. Offer simple, honest framing. “Babies pick up microbes from many sources, in the first days and over the first years, and research is still learning what matters for health.”
3. Point to practical, low-risk habits. Skin-to-skin contact, responsive feeding and the family’s own decisions about feeding, all supported on their own merits.
4. Refer questions about interventions. Seeding, probiotics and testing go to the obstetric or pediatric provider.
5. Link to related content. See Combination Feeding: Supporting Families Without Judgment or Misinformation for feeding choices.

Limits and uncertainty

Most evidence on the infant microbiome is observational, based on stool samples, an indirect measure of the gut, in cohorts that differ in geography, diet and sequencing methods. The strain-level study included 25 pairs, the TEDDY cohort was assembled for diabetes research, and the seeding randomized trial included 20 neonates. Effects on diversity are conflicting between studies, and no reviewed abstract reported a clinical outcome such as asthma or allergy. This article draws on abstracts only, and evidence on probiotics, prebiotics, antibiotic exposure and maternal diet (active areas of research) was not reviewed. Guidance can change as larger trials report.

The bottom line

Birth and feeding practices are associated with differences in the infant gut microbiome, with breastfeeding and vaginal birth linked to particular microbes in large cohort data. Whether changing the microbiome changes health is not established, and procedures such as vaginal seeding remain research-only according to ACOG. A doula can share the evidence accurately, avoid guilt or promises, support well-established feeding practices and refer questions about interventions to clinicians.

Birth & Baby University’s For Doulas page outlines its birth doula training, postpartum doula training, recertification and mentorship for doulas who support families through birth and the newborn weeks. Confirm that any program meets your certifier’s, employer’s or state’s requirements before you enroll.

This article is for professional education. It is not medical, legal or tax advice. Check the standards of your certifying organization and the rules where you work. For concerns about a baby’s health, contact a pediatric provider or emergency services.

Sources and further reading

• Ferretti P, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host & Microbe (2018). Read the source
• Stewart CJ, et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature (2018). Read the source
• American College of Obstetricians and Gynecologists. Committee Opinion No. 725: Vaginal seeding. Obstetrics & Gynecology (2017). Read the source
• Mueller NT, et al. Maternal bacterial engraftment in multiple body sites of cesarean section born neonates after vaginal seeding: a randomized controlled trial. mBio (2023). Read the source
• Wang X, et al. Impact of vaginal seeding on the gut microbiome of infants born via cesarean section: a systematic review. Journal of Infection (2024). Read the source

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