Helping Your Child Develop a Healthy Microbiome

Sasha Milbeck, National Center for Health Research

What Is the Microbiome?

The microbiome is a system of up to 10,000 different helpful microorganisms that call our bodies home, with the largest amounts found in the intestines, skin, mouth, and vagina.[1] These microorganisms help the immune system develop and fight infection from harmful bacteria and viruses, digest food, and assist with the daily operations of the human body. To learn more about the different microorganisms that live in your body, click here.

Microbiome research is a new and quickly growing field. We still know very little about the microbiome in general and how it develops in children in particular. There has been some recent research that suggests that babies born vaginally have different microbiomes compared to babies born via caesarean section (C-section). This article will mainly focus on ways to promote microbiome development in children, specifying when there is good research evidence (such as breastfeeding) and when we don’t yet have enough research evidence (such as fecal matter transfers and vaginal seeding procedures).

How Babies Develop a Microbiome

Until recently, research was inconclusive about when the gut acquires the necessary microbes. It was previously thought that maternal microbes do not pass across the placenta, and that babies are born without a microbiome. However, we now know that babies are born with some microbes in their gut, although most are acquired after delivery.[2] The transfer of bacteria from a mother to an infant occurs during birth, skin-to-skin contact after birth, and breastfeeding.

Exposure to different microorganisms shapes our microbiomes. Babies who are born vaginally pass through their mother’s birth canal and are exposed to their mother’s vaginal and fecal bacteria. The mother’s bacteria enter the babies’ guts and help support their development of a healthy microbiome.[3]

C-sections and Microbiome Differences

Babies born via C-section do not pass through the birth canal, so they are not exposed to the same microbes as babies born vaginally. In 2019, researchers in the United Kingdom conducted the largest ever study of the newborn microbiome. The results showed that babies born via C-section lack strains of gut bacteria found in healthy children and adults, and instead have higher amounts of harmful bacteria found in hospital operating rooms.[4]

The type of bacteria found in the gut microbiome during the first 100 days after delivery has been shown to predict certain health conditions, such as asthma. Researchers from the Canadian Healthy Infant Longitudinal Development Study found that children with asthma had fewer of a type bacteria named Lachnospira, and more bacteria Clostridium neonatale bacteria.[5] Infants born via C-section are known to have more Clostridium bacteria within the first 3 weeks of life. But, we still don’t know if that means that babies born by C-section are more likely to develop childhood asthma. These study results also don’t tell us if particular microorganisms protect against immune disorders. For additional information on whether bacteria can support the immune system in allergy and asthma prevention, click here.

Other studies have linked C-sections to increased chances of developing allergies, autoimmune diseases, and other health conditions, which could be due to babies born by C-section not being exposed to their mother’s vaginal and fecal bacteria. To learn more about the health risks associated with being born via C-section, click here. While C-section birth has been linked to numerous health conditions in babies, that does not mean all babies born via C-section will have health problems as children or adults.

It is important to note that these studies were conducted on babies who are born via elective C-sections, and not emergency C-sections (those done because of failed labor or other stress to the newborn). For that reason, the results suggest that the lack of contact between the baby and the mother’s vagina during childbirth can have a significant effect on the baby’s microbiome, even during a healthy pregnancy and uneventful childbirth.[6] 

Promoting a Child’s Healthy Microbiome Development

Not every baby delivered by C-section develops a dangerously inadequate microbiome or related health problems. The most promising methods for successful microbiome development are skin-to-skin contact with a baby after delivery, avoiding unnecessary antibiotics while pregnant, giving your baby probiotic supplements, and breastfeeding your child.[7]

Benefits of Breastfeeding

The American Academy of Pediatrics recommends exclusively breastfeeding babies for the first 6 months of life and continuing to breastfeed until the baby is 1 year old.[8] Breastfeeding offers many benefits for a mother and baby, including protection from disease for both mother and child, defense against childhood obesity, and helping mothers lose weight gained during pregnancy. To learn more about the benefits of breastfeeding, click here.

The amount of mother’s breast milk that a baby drinks daily may influence the diversity and health of the baby’s microbiome. A 2017 study found that the amount of the healthy bacteria in babies’ guts (which may predict a decreased likelihood of developing allergic diseases and asthma) was proportionately linked to amount of daily breast milk.[9] This benefit of more breast milk on babies’ gut microbiome was maintained even after babies began eating solid foods.  Although the research is not conclusive, experts believe that there could be benefits and there are no risks of breastfeeding in a baby’s development of a healthy microbiome.

Antibiotics and Probiotics

Antibiotics are intended to kill dangerous bacteria, but they also can kill healthy gut bacteria.  While antibiotics can be life-saving, overuse in children may be harmful to children’s gut bacteria and be associated with chronic and autoimmune disorders, and antibiotic resistant infections such as MRSA.[10,11] Read more about antibiotic-resistant bacteria here or here. Antibiotics should only be used to fight bacterial infections, not for colds, the flu, or ear infections that are caused by viruses.

Probiotics are live microorganisms that are marketed to help restore the gut microbiome, protect us against inflammation, and support our immune system.[12] Numerous studies found that supplementing babies’ breastfeed with Bifidobacteria, a type of bacteria that digests breast milk, protects against harmful bacteria, and makes up about 80-90% of the infant microbiome, was associated with reduced autoimmune and childhood diseases.[13,14] Absence of Bifidobacteria was also linked to increased gut inflammation and allergies in babies and infants.[15,16] However, all of these studies only focused on how probiotics affect babies and very young children. It is not known whether probiotics have a lasting benefit on the microbiome later in life. If you’re considering a probiotic supplement for your child, we suggest that you talk to your health care provider about other ways to support your child’s microbiome that have been proven true by more research.

Vaginal Seeding and Fecal Transfers: What are the Risks and Benefits?

Some women who deliver their babies via C-section consider adding healthy bacteria to their babies’ microbiomes through procedures called vaginal seeding and fecal matter transfers. While preliminary research suggests these procedures might possibly be beneficial, they are not recommended by physicians or the FDA at this time, because more research is needed to evaluate the long-term risks and benefits.

Vaginal Seeding

Vaginal seeding is a procedure where a cotton swab is coated with fluids from the mother’s vagina, and transferred to the mouth, nose, or skin of a newborn infant. The intended purpose is to transfer a mother’s vaginal bacteria to a baby delivered via C-section, to add healthy bacteria to the fetal microbiome with the goal of reducing future health problems.

A 2016 study of 18 infants (7 born vaginally and 11 born via C-section), was designed to determine the benefits of vaginal seeding on C-section babies.[17] Four of the 11 babies born via C-Section received vaginal seeding. A month later, researchers found that the microbiomes of the infants who had the vaginal seeding procedure had bacteria typically found in the vaginas of the mother and in the guts of vaginally born babies. These results are promising, but since it is just one very small study, more research is needed on more babies to determine the benefits or risks of vaginal seeding.

Currently, the American College of Obstetricians and Gynecologists does not recommend or encourage vaginal seeding procedures outside of medical clinical trials.[18] The mothers in the study were screened for infections, sexually transmitted infections (STIs), and abnormal bacterial overgrowth in the vagina.  Among a general population of pregnant women, undiagnosed STIs and bacterial and viral infections can cause serious infections in a newborn and lead to lifelong illnesses and disabilities. For that reason, we agree that the risks and benefits of vaginal seeding will not be known until better research has been completed.

Fecal Matter Transfers

Fecal matter transfers (FMT) consist of taking stool samples from a healthy donor (screened for medical conditions that can be transferred through stool) and placing them into the gut of another person. FMT has been done to help reintroduce good bacteria that is missing from a patient’s gut. Currently, the FDA only approves of FMT being conducted in a medical setting or as part of a clinical research study. To learn more about the risks and benefits of FMT, click here.

An 2020 study investigated whether FMT can introduce healthy bacteria to the gut microbiomes of babies born via C-section.[19] Babies delivered by C-section were given a dose of live fecal bacteria in their first bottle of milk, and their health was monitored for two days, with follow-up visits at four weeks and three months. The gut microbiota of babies who received FMT were similar to babies born vaginally, and were distinctly different from untreated C-section babies and from C-section babies who received vaginal seeding.

As is the case with vaginal seeding, larger and longer-term studies are needed to determine the safety of the procedure and determine if there are any long-term health benefits. At this point, physicians and other experts do not encourage mothers to try the FMT procedure on their newborns.

Bottom Line

Microbiome research is a new and quickly developing area of research. We now know that babies are born with some microbes in their gut, but quickly acquire most of their microbes after birth. Numerous new studies suggest that C-sections affect a baby’s gut microbiome. Although some studies show that a treatment may seem promising, that doesn’t mean the treatment is safe or effective. Don’t embrace a new procedure just because you heard or read that it was a good idea. Talk to your physician about what you can do to support your baby’s development of a healthy microbiome and immune system if you are planning a C-section delivery.

All articles are reviewed and approved by Dr. Diana Zuckerman and other senior staff.

The National Center for Health Research is a nonprofit, nonpartisan research, education and advocacy organization that analyzes and explains the latest medical research and speaks out on policies and programs. We do not accept funding from pharmaceutical companies or medical device manufacturers. Find out how you can support us here.


  1. “Your Microbes and You.” National Institutes of Health, U.S. Department of Health and Human Services, 10 Jan. 2018,
  2. Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014). The placenta harbors a unique microbiome. Science Translational Medicine, 6(237), 237ra65.
  3. Ferretti P, Pasolli E, Tett A, et al. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host & Microbe. 2018;24(1):133-145.e5. doi:10.1016/j.chom.2018.06.005
  4. Shao, Y., Forster, S.C., Tsaliki, E. et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 574, 117–121 (2019).
  5. Stiemsma LT, Arrieta MC, Dimitriu PA, et al. Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma. Clinical Science. 2016;130(23):2199-2207. doi:10.1042/CS20160349
  6. Dunn AB, Jordan S, Baker BJ, Carlson NS. The Maternal Infant Microbiome: Considerations for Labor and Birth. The American Journal of Maternal/Child Nursing. 2017;42(6):318-325. doi:10.1097/NMC.0000000000000373
  7. Tamburini, S., Shen, N., Wu, H. et al. The microbiome in early life: implications for health outcomes. Nature Medicine 22, 713–722 (2016).
  8. Section on Breastfeeding. Breastfeeding and the use of human milk. Pediatrics. 2012 Mar;129(3):e827-41. doi: 10.1542/peds.2011-3552. Epub 2012 Feb 27. PMID: 22371471.
  9. Pannaraj PS, Li F, Cerini C, et al. Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome. JAMA Pediatrics. 2017;171(7):647–654. doi:10.1001/jamapediatrics.2017.0378
  10. Iizumi T, Battaglia T, Ruiz V, Perez Perez GI. Gut Microbiome and Antibiotics. Archives of Medical Research. 2017;48(8):727-734. doi:10.1016/j.arcmed.2017.11.004
  11. Aversa Z, Atkinson EJ, Schafer MJ, et al. Association of Infant Antibiotic Exposure With Childhood Health Outcomes [published online ahead of print, 2020 Nov 6]. Mayo Clinic Proceedings. 2020;S0025-6196(20)30785-0. doi:10.1016/j.mayocp.2020.07.019
  12. Butel MJ. Probiotics, gut microbiota and health. Médecine et maladies infectieuses. 2014;44(1):1-8. doi:10.1016/j.medmal.2013.10.002
  13. Di Gioia D, Aloisio I, Mazzola G, Biavati B. Bifidobacteria: their impact on gut microbiota composition and their applications as probiotics in infants. Applied Microbiology & Biotechnology. 2014;98(2):563-577. doi:10.1007/s00253-013-5405-9
  14. Cukrowska B, Bierła JB, Zakrzewska M, Klukowski M, Maciorkowska E. The Relationship between the Infant Gut Microbiota and Allergy. The Role of Bifidobacterium breve and Prebiotic Oligosaccharides in the Activation of Anti-Allergic Mechanisms in Early Life. Nutrients. 2020;12(4):946. Published 2020 Mar 29. doi:10.3390/nu12040946
  15. Henrick, B.M., Chew, S., Casaburi, G. et al. Colonization by B. infantis EVC001 modulates enteric inflammation in exclusively breastfed infants. Pediatric Research 86, 749–757 (2019).
  16. Pizano JM, Williamson CB, Dolan KE, et al. Probiotics and Disease: A Comprehensive Summary-Part 7, Immune Disorders. Integrative Medicine (Encinitas). 2017;16(5):46-57.
  17. Dominguez-Bello, M., De Jesus-Laboy, K., Shen, N. et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine 22, 250–253 (2016).
  18. Vaginal Seeding. (n.d.). Retrieved from
  19. Korpela, K., Helve, O., Kolho, K., Saisto, T., Skogberg, K., Dikareva, E., . . . Vos, W. M. (2020). Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study. Cell, 183(2). doi:10.1016/j.cell.2020.08.047