Blog

C-section Birth & the Microbiome

May 18, 2022 17 min readBy Entegro Health

If you had a cesarean and you've read something worrying about your baby's gut bacteria, this is the article for you. The research is real — and the part that gets left out is the reassuring part.

A mother cradling her newborn baby in her arms at home

Giving birth is one of the most profound things a person can do, and it happens somewhere in the world every second of every day. It can also be one of the most overwhelming — particularly when the plan changes on the day.

Cesarean birth is common and getting more so. WHO reported in 2021 that cesareans account for more than one in five births worldwide, projected to reach nearly a third by 2030.^1,2 In the United States the rate was 32.5% in 2025 — about one baby in three.³ A lot of research has followed those babies around, and some of it has been reported in a way that would frighten anyone.

So let's go through what the studies actually found, including the parts that usually get cut.

First, the birth itself

A newborn baby sleeping in a hospital bassinet with their mother standing beside them

A cesarean is major abdominal surgery: the baby is delivered through incisions in the abdomen and uterus. It is not, as the phrase goes, the easy way out — a point worth making since somebody usually says it.

Some are planned. Many are not: the need for a first cesarean often isn't known until labor is already underway. Common reasons include labor not progressing, concern about the baby's wellbeing, the baby lying in an awkward position, twins or more, problems with the placenta, a prolapsed cord, an obstruction, a previous cesarean or uterine surgery, and certain maternal infections or health conditions.⁴

Cesareans save lives, and where they're unavailable, women and babies die. What obstetric bodies discourage is the cesarean performed with no medical reason at all, because it carries the risks any major surgery carries.²

Where does "cesarean" come from?

Nobody knows, which is a more entertaining answer than the one you've heard. The National Library of Medicine's history of the procedure notes the popular Julius Caesar story is unlikely — his mother Aurelia is reputed to have lived long enough to hear of his invasion of Britain, and surviving the operation in 100 BC was not on the cards. Other candidates include Roman law and the Latin verb caedare, to cut. The NLM's own conclusion: "we cannot be sure of where or when the term cesarean was derived."⁵

Can you give birth again afterwards?

Yes. Both a planned repeat cesarean and a vaginal birth after cesarean are options, and which is safer depends on why the first one happened — a conversation for your provider rather than the internet.⁶

On timing: ACOG and the Society for Maternal-Fetal Medicine advise avoiding intervals shorter than six months between pregnancies, and discussing the risks and benefits of intervals shorter than eighteen months.⁷ WHO suggests waiting at least twenty-four months.⁸ If you're hoping for a vaginal birth next time, a longer gap is associated with a better chance of it working.⁶ Your age, your health and how the surgery healed matter more than any single number.

What the microbiome research actually found

A newborn's gut goes from more or less empty to densely populated in a matter of days. In the words of the study most often cited on this: "immediately after birth, newborn babies experience rapid colonization by microorganisms from their mothers and the surrounding environment."⁹

That study is the UK Baby Biome Study, published in Nature in 2019: 596 full-term babies, 314 born vaginally and 282 by cesarean, with 1,679 stool samples sequenced.⁹ It is the source of nearly every headline you've read on this subject, so it's worth knowing what it says.

In the first weeks, babies born vaginally were much more likely to carry high levels of Bacteroides — a group of ordinary, useful gut bacteria — picked up from their mothers. Cesarean-born babies mostly didn't. Instead, their early gut communities carried more of what the researchers called opportunistic organisms, the sorts of bacteria common in hospitals: about 30% of the species present in the first three weeks, against about 10% in vaginally born babies.⁹

That's the part that made the news. Here's the part that didn't.

The same researchers went back at around nine months

By then the gap had very nearly closed. The amount of variation between babies explained by how they were born fell from 7.6% at four days to 1.0% by infancy. The opportunistic organisms had dropped from 30% versus 10% to 2.8% versus 1.6%. And the difference had narrowed to a single group of bacteria — Bacteroides — rather than a whole community.⁹

A separate randomized trial that followed children all the way to age three put it more simply still: the differences between cesarean-born and vaginally born children "could not be observed at 3 years of age."¹⁰ Even the study titles in this field have shifted toward the right word: a 2020 analysis of 132 newborns called it a delayed establishment of the gut microbiota, not a failed one.³⁰

And the authors of the 2019 study were careful about what they had and hadn't measured: the clinical consequences of these early differences, they wrote, "remain to be determined." They counted bacteria. They did not measure a single illness.⁹

Your baby wasn't born with the wrong bacteria. What the research describes is a difference in timing.

And the reason isn't what almost everyone says it is

You will have read that the difference comes from the baby missing a dose of the mother's vaginal bacteria on the way out. It's a tidy story, it is repeated everywhere, and the Baby Biome Study looked for it and couldn't find it.

The researchers found no meaningful difference in Lactobacillus — the genus that dominates the vaginal microbiome — between the two groups of babies. What differed was Bacteroides, Bifidobacterium and E. coli: organisms that come from the mother's gut, not her vagina.⁹ A 2026 Nature study of 714 mother-and-baby pairs, with more than 4,500 samples, reached the same conclusion — the maternal gut is the major reservoir, with only occasional transmission from vaginal or breast-milk microbiomes.¹¹

The antibiotics have also been tested, which is more than most articles will tell you. Mothers receive antibiotics before a cesarean to prevent infection, and it was long assumed this was a second hit on the baby's gut. Two randomized trials have now compared giving them before the incision against giving them after the cord is clamped. Neither found a meaningful difference in the baby's microbiome.^10,12 The antibiotics protect the mother, which matters to the baby too.

What about asthma and allergies?

This is the worry underneath the worry, so let's take it properly.

There is a real, consistently observed association. The most comprehensive review to date pooled 113 studies and found modestly raised odds for children born by cesarean: asthma 1.20, allergic rhinitis 1.15, eczema 1.08, food allergy 1.35.¹³ Small increases in relative terms, and smaller still in absolute ones. One survey of 12,639 Shanghai schoolchildren also reported that the association was not significant among children who had been breastfed in early infancy — though it asked parents to recall both the birth and the diagnosis years later, and its authors put it no more strongly than breastfeeding "may attenuate" the risk.²⁸

Association isn't cause, and here the gap is unusually well studied

Families who have cesareans differ from families who don't, in ways that also affect asthma. The clean way to test that is to compare siblings born by different routes to the same mother. A Swedish study of 87,500 sibling pairs found the effect of planned cesarean on asthma disappeared in the sibling comparison, and concluded that the explanation should be sought in "the indications for emergency CS" rather than in vaginal bacteria.¹⁴ A second Swedish analysis of nearly 200,000 children found the association held to age five and was gone by six to nine.¹⁵ Cleanest of all: 464 twin pairs where one twin was born vaginally and the other by emergency cesarean, minutes apart, found no association with childhood asthma.¹⁶

In fairness, this is contested. A 2023 meta-analysis of nearly 22 million people argues sibling designs over-correct and hide a real effect.¹⁷ The honest summary: the association is real and small, causation is unproven, and the specific mechanism people usually blame — the missed vaginal bacteria — is the one the evidence contradicts.

What genuinely helps, and you may already be doing it

A newborn baby breastfeeding, cradled in their mother's arm

Here is the genuinely useful finding, and it's a good one.

When the same research team expanded the Baby Biome Study to 1,288 babies and looked at what actually predicted a stable, resilient infant gut, the answer wasn't how the baby was born. It was Bifidobacterium — and the thing that drives Bifidobacterium is a diet rich in breast milk.¹⁸ Babies whose gut communities were dominated by B. breve and B. longum showed long-term resistance to problem bacteria.

The reason is elegant. Human milk contains sugars called human milk oligosaccharides that your baby cannot digest at all. They aren't for the baby — they're food for the bacteria, and specifically for bifidobacteria.¹⁹ The milk arrives with the meal for the microbes included.

In the 2024 Dutch trial data, feeding mode came out as the dominant factor shaping the infant gut — ahead of antibiotics, and doing more work than delivery mode by the end of the first year.¹² Skin-to-skin contact, feeding, and time are doing most of it.

And if breastfeeding doesn't work out — because of the surgery, the pain relief, the delay, the supply, or any of the other reasons it doesn't always work — that is not a door closing. The differences narrow anyway. They narrowed in every study above, including for the formula-fed babies in them.

What about vaginal seeding?

You may have seen this: swabbing the mother's vaginal microbiome onto a cesarean-born baby's mouth, nose and skin, to give the baby the exposure it missed. It's an appealing idea, it has been tested, and the results have not been kind to it.

The idea came from a 2016 pilot in which just four babies were swabbed, and which its own authors described as achieving only partial restoration, with long-term health consequences unclear.²⁹
A randomized trial that followed 120 babies for two years found vaginal seeding had "no significant impacts on the gut microbiota, growth, or allergy risks."²⁰
A randomized pilot found no difference in gut microbiome composition at one or three months, and that transfer of the mother's vaginal strains was "rare" — leading the authors to question the value of the practice.²¹
Which fits everything above: the bacteria that transfer are from the mother's gut, not her vagina.^9,11

What ACOG says, reaffirmed in 2025

The American College of Obstetricians and Gynecologists "does not recommend or encourage vaginal seeding outside of the context of an institutional review board-approved research protocol," and recommends it "otherwise not be performed until adequate data regarding the safety and benefit of the process become available."²²

If a mother still wishes to do it, ACOG asks for a thorough discussion of the risk of passing on infection, testing for herpes simplex, group B streptococcus, chlamydia and gonorrhea, documentation of that conversation, and that the baby's pediatrician be told it was done.²²

Probiotics and babies: please read this bit

We sell probiotics, so we'll be direct: a probiotic is not something to give a newborn on the strength of a blog post — including this one.

Talk to your pediatrician first — before any product, ours included

The FDA has approved no probiotic for use in infants of any age, and in 2023 it warned health care providers that preterm infants given probiotics are at risk of invasive, potentially fatal disease caused by the organisms in them, after a premature baby died of sepsis traced by genetic sequencing to the product it had been given.²³ In 2014 a premature infant died of a fungal infection traced to a contaminated retail probiotic supplement, which was recalled.²⁴

Those cases involved premature and hospitalised babies, and a healthy full-term baby at home is a different situation. But this is a decision for your baby's doctor, not for a website. Do not give a probiotic to an infant who is premature or low birth weight, is in hospital, has a central line or feeding tube, has had bowel surgery, is immunocompromised, or is taking antibiotics — unless a clinician has specifically told you to.

The American Academy of Pediatrics is equally plain about the strongest evidence base there is, in preterm infants: current evidence "does not support the routine, universal administration of probiotics to preterm infants."²⁵ And a 2022 systematic review of supplements given after cesarean birth concluded it is "yet too early to advocate specific products in clinical settings."²⁶

Where Flourish fits

A pregnant woman resting her hands on her bump, seated beside two bottles of Entegro Health Flourish probiotic

With you, not with your baby.

Flourish is a living liquid probiotic taken daily by adults to support digestive and microbiome health — eleven strains from five families, fermented together as one culture, third-party tested every batch. Recovering from abdominal surgery while feeding a newborn is a lot to ask of a body, and a daily habit that supports your own digestion is a reasonable thing to want.

What we won't tell you is that it does anything for your baby's microbiome, because nobody has tested that. Anyone who does tell you that is ahead of the evidence.

Flourish is a dietary supplement made to support digestive and microbiome health. It is not a treatment for any condition, and it is not intended to affect an infant's microbiome or to prevent allergy, asthma or any other disease. If you are pregnant, breastfeeding, or considering a supplement for a child of any age, speak to your healthcare provider before starting — and follow the dosage on the label.

Ready to try a living probiotic?

Eleven living strains. One shared culture. One daily shot, for grown-ups.

Shop Flourish Original · What's inside · Product FAQ

A few questions we hear a lot

Did my cesarean damage my baby's microbiome?

No. The research describes a difference in which bacteria arrive first and how quickly, not damage. By around nine months the difference had shrunk to a single group of bacteria, and by three years one trial couldn't detect it at all.^9,10 No study has shown those early differences making a child ill.

Should I ask for vaginal seeding?

ACOG says not outside approved research, a position it reaffirmed in 2025, and the trials have been null.^20,21,22 If you're still considering it, take the conversation to your obstetric provider, who can arrange the infection testing ACOG asks for.

Can I give my baby a probiotic?

Ask your pediatrician before you buy anything, from us or anyone else. The FDA has approved no probiotic for infants of any age, and there are documented infant deaths involving probiotic products in vulnerable babies.^23,24

I couldn't breastfeed. Have I missed the window?

No. Human milk feeds bifidobacteria particularly well, which is why it comes up so often in this research — but the studies that followed cesarean-born babies to nine months and three years included formula-fed babies, and the differences narrowed anyway.^9,10 Any amount of breast milk counts, and no amount is not a failure.

Is there anything I can actually do?

Skin-to-skin contact, feeding your baby however feeding is working, and not reaching for antibiotics unless they're needed. Beyond that, time is doing the work, and it does it without your supervision.

Was my baby's microbiome already forming before birth?

Probably not. A large 2023 review in Nature concluded that reports of a "fetal microbiome" are most likely contamination, and that a healthy fetus is not stably colonized.²⁷ Colonization starts at birth.

About this article

Written by: Kelsy Armstrong, Entegro Health | Originally published: May 2022

Important information

This article is for general education and is not a substitute for professional medical advice, diagnosis, or treatment. Decisions about delivery, feeding, and anything given to an infant should be made with your obstetric provider and your child's pediatrician. Much of the research described here is observational and cannot establish cause, and the microbiome studies measured bacteria rather than health outcomes. Probiotic effects are specific to the strain, the dose and the population studied; evidence for one product does not transfer to another, and evidence from infant formula trials does not transfer to dietary supplements. These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease.

Sources

World Health Organization (16 June 2021). Caesarean section rates continue to rise, amid growing inequalities in access. Source
Betrán, A. P., Ye, J., Moller, A.-B., Souza, J. P., & Zhang, J. (2021). Trends and projections of caesarean section rates: global and regional estimates. BMJ Global Health, 6(6), e005671 — 154 countries; 21.1% globally, projected 28.5% by 2030. Source
Hamilton, B. E., Osterman, M. J. K., & Gregory, E. C. W. (2026). Births: provisional data for 2025. Vital Statistics Rapid Release, no. 43. National Center for Health Statistics — cesarean delivery rate 32.5%. Source
Mayo Clinic. C-section — why it's done, risks, and what to expect. Source
U.S. National Library of Medicine. Cesarean Section — A Brief History, Part 1 — "we cannot be sure of where or when the term cesarean was derived." Source
American College of Obstetricians and Gynecologists (2019). Practice Bulletin No. 205: Vaginal birth after cesarean delivery. Obstetrics & Gynecology, 133(2), e110–e127. Source
American College of Obstetricians and Gynecologists & Society for Maternal-Fetal Medicine (2019). Obstetric Care Consensus No. 8: Interpregnancy care. Obstetrics & Gynecology, 133(1), e51–e72. Source
World Health Organization (2007). Report of a WHO Technical Consultation on Birth Spacing, Geneva, 13–15 June 2005. Source
Shao, Y., Forster, S. C., Tsaliki, E., et al. (2019). Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature, 574(7776), 117–121 — the UK Baby Biome Study; 596 babies, re-sampled at about nine months. Source
Dierikx, T., Berkhout, D., Eck, A., et al. (2022). Influence of timing of maternal antibiotic administration during caesarean section on infant microbial colonisation: a randomised controlled trial. Gut, 71(9), 1803–1811 — differences "could not be observed at 3 years of age." Source
Sinha, T., Brushett, S., Fernández-Pato, A., et al. (2026). Maternal influences on infant gut microbiome and health. Nature — 714 mother–infant pairs; the maternal gut is the major reservoir. Source
Sinha, T., Prins, J. R., Fernández-Pato, A., et al. (2024). Maternal antibiotic prophylaxis during cesarean section has a limited impact on the infant gut microbiome. Cell Host & Microbe, 32(8), 1444–1454 — feeding mode was the predominant factor. Source
Liu, X., Zhou, J., Chen, J., et al. (2024). Risk of asthma and allergies in children delivered by cesarean section: a comprehensive systematic review. The Journal of Allergy and Clinical Immunology: In Practice, 12(10), 2764–2773 — 113 studies. Source
Almqvist, C., Cnattingius, S., Lichtenstein, P., & Lundholm, C. (2012). The impact of birth mode of delivery on childhood asthma and allergic diseases — a sibling study. Clinical & Experimental Allergy, 42(9), 1369–1376 — 87,500 sibling pairs. Source
Bråbäck, L., Ekéus, C., Lowe, A. J., & Hjern, A. (2013). Confounding with familial determinants affects the association between mode of delivery and childhood asthma medication. Allergy, Asthma & Clinical Immunology, 9(1), 14 — 199,837 children. Source
Brix, N., Stokholm, L., Jonsdottir, F., Kristensen, K., & Secher, N. J. (2017). Comparable risk of childhood asthma after vaginal delivery and emergency caesarean section. Danish Medical Journal, 64(1), A5313 — 464 twin pairs. Source
Yu, H. Z., Wang, X. W., Guo, Z. Y., et al. (2023). Association of caesarean delivery with offspring health outcomes in full-cohort versus sibling-comparison studies. BMC Medicine, 21(1), 348 — argues sibling designs under-adjust. Source
Shao, Y., Garcia-Mauriño, C., Clare, S., et al. (2024). Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. Nature Microbiology, 9(10), 2570–2582 — 1,288 UK neonates. Source
Bode, L. (2009). Human milk oligosaccharides: prebiotics and beyond. Nutrition Reviews, 67(Suppl. 2), S183–S191. Source
Liu, Y., Li, H.-T., Zhou, S.-J., et al. (2023). Effects of vaginal seeding on gut microbiota, body mass index, and allergy risks in infants born through cesarean delivery: a randomized clinical trial. American Journal of Obstetrics & Gynecology MFM, 5(1), 100793 — 120 infants, two-year follow-up, null. Source
Wilson, B. C., Butler, É. M., Grigg, C. P., et al. (2021). Oral administration of maternal vaginal microbes at birth to restore gut microbiome development in infants born by caesarean section: a pilot randomised placebo-controlled trial. eBioMedicine, 69, 103443. Source
American College of Obstetricians and Gynecologists (2017, reaffirmed 2025). Committee Opinion No. 725: Vaginal seeding. Obstetrics & Gynecology, 130(5), e274–e278. Source
U.S. Food and Drug Administration (2023). FDA raises concerns about probiotic products sold for use in hospitalized preterm infants; and Letter to Health Care Providers: Risk of Invasive Disease in Preterm Infants Given Probiotics. Source
Vallabhaneni, S., Walker, T. A., Lockhart, S. R., et al. (2015). Notes from the field: fatal gastrointestinal mucormycosis in a premature infant associated with a contaminated dietary supplement — Connecticut, 2014. MMWR, 64(6), 155–156. Source
Poindexter, B.; Committee on Fetus and Newborn (2021). Use of probiotics in preterm infants. Pediatrics, 147(6), e2021051485. Source
Carpay, N. C., Kamphorst, K., de Meij, T. G. J., et al. (2022). Microbial effects of prebiotics, probiotics and synbiotics after caesarean section or exposure to antibiotics in the first week of life: a systematic review. PLOS ONE, 17(11), e0277405. Source
Kennedy, K. M., de Goffau, M. C., Perez-Muñoz, M. E., et al. (2023). Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature, 613(7945), 639–649. Source
Chu, S., Zhang, Y., Jiang, Y., et al. (2017). Cesarean section without medical indication and risks of childhood allergic disorder, attenuated by breastfeeding. Scientific Reports, 7, 9762 — a cross-sectional parent-reported survey of 12,639 Shanghai schoolchildren; the authors conclude breastfeeding "may attenuate" the risks. Source
Dominguez-Bello, M. G., De Jesus-Laboy, K. M., Shen, N., et al. (2016). Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine, 22(3), 250–253 — the original pilot; 18 infants, 4 seeded. Source
Kim, G., Bae, J., Kim, M. J., et al. (2020). Delayed establishment of gut microbiota in infants delivered by cesarean section. Frontiers in Microbiology, 11, 2099 — 132 Korean newborns sampled on days 3, 7 and 14. Source