are c-sections safe for baby microbiomes?

C-Sections vs. Vaginal Delivery: What's Better for an Infant's Health?

The belief that C-sections destroy a baby’s chance at a healthy microbiome has become a popular one. This common narrative may not be as clear as we once thought, though. Science about microorganisms and C-sections have come a long way. The incoming (or outgoing?) baby may still get some exposure to protective microbes even through this almost-routine procedure. Let's discuss bacterial communities in the vaginal microbiome and the exposure to healthy bacteria for children through vaginal delivery and C-section.

Vaginal Delivery vs. C-Section: What's Better for Baby Health?

When the baby passes through the vaginal microbiome, your incoming bundle of joy gets exposed to a plethora of bacteria [1]. The common idea is that this initial exposure of the baby to the vaginal microbiota is pivotal in setting the trajectory for the baby’s health.

This belief system is part of the hygiene hypothesis. While there is some credibility regarding delivery type within the hygiene hypothesis, it doesn’t mean a baby born via C-section is doomed.

Numerous health-conscious mothers want the immune-boosting support of a vaginal delivery. However, many women prefer the comfort of a C-section. Others must choose this delivery method for health reasons.

No matter what, it’s a woman’s choice. They shouldn’t feel pressured to sway either way. However, these decision-makers should have all the facts.

Thankfully, our knowledge about C-sections is broadening. Not all C-sections are created equal. In fact, some C-sections still expose your baby to healthy gut bacteria!

Health Risks Associated with C-Sections

There are a lot of health risks for babies associated with getting a C-section.

In fact, babies who are products of C-sections have been linked to:

  • Autoimmune Diseases [2]
  • Asthma [3]
  • Type 1 Diabetes [4]
  • Celiac Disease [5]
  • Obesity [6]

While these statistics may be alarming, each situation is unique. Mothers have their own set of DNA, bacteria, and immune cells that they transfer to their children. These traits have essential implications for all factors of our health. These very influencers can also be the reason why a C-section might be necessary. 

The Uniqueness of the Vaginal Microbiome 

That's what makes microbiology so interesting! The human vagina has hundreds of bacterial species that make each situation unique.

For the most part, these microbes are pretty helpful. These flora regulate vaginal pH to ensure pathogens don't take over and help regulate immune responses in the area. 

However, different bacteria can cause infertility issues, preterm delivery, bacterial vaginosis (BV), or a vaginal infection that requires medical intervention. 

That's why decisions about your baby's health and vaginal health are so personal and need to be made with as much information presented as possible.

What Are the Differences in Microbiomes Between the Babies Born Through C-section and Those Born Through the Vagina?

Babies do not live in a sterile environment like we once thought. Bacteria are found throughout the womb. Not to mention, there are gut bacteria in a baby’s first bowel movement. Yeah, those sometimes occur inside the uterus!

An analysis of the vaginal microbiome found,

"Human amniotic fluid and placenta harbour unique microbial communities, which may provide the initial inoculum for gut colonisation, the single most important determinant of host-microbe interaction modulating the risk of non-communicable disease [7] ."

- Nature

These findings show that a baby’s exposure to bacteria through vaginal microbial communities happens before the child is even born. Additionally, after the amniotic sac (which is the sac of water the fetus is held in) breaks, the baby begins to be exposed to bacteria in the vaginal microbiome.

One meta-analysis compared the anaerobic bacteria of infant children. Some were born via C-section, while others were delivered vaginally.

Results found,

"Caesarean section is characterized by lower numbers of strict anaerobes such as Bacteroides fragilis and bifidobacteria compared to vaginally delivered infants [8]."

- Clin Med Pediatr

Research suggests that babies whose mother’s water broke prior to a C-section being performed had more microbial biodiversity than children born of a C-section whose mother’s water didn’t break [9].

Even if the result of the birth is a C-section, the broken amniotic sac allows some bacterial exposure from vaginal flora. This partial greeting between the fetus and microbes affects the baby’s microbiome. In particular, the vaginal microbiome is teeming with many species of Lactobacillus. 

Vaginal lactobacilli are essential for keeping yeast infections to a minimum and protecting against pathogens. They are among the first in the vaginal ecosystem to greet your little one. If you choose to breastfeed, you will continue to pass on various Lactobacillus species to your child that will help keep their immune system and digestive system healthy. 

Vaginal Microbiome and Labor

Labor is when a woman’s body begins to prepare for childbirth. In a nutshell, The labor process includes massive hormonal shifts [10].

When these changes happen, it causes:

  • Contractions of the Uterus
  •  Dilation of the Cervix
  • Amniotic Sac Rupturing (Water Breaking)

All of these changes don’t just affect mom. As the process continues, the fetus is exposed to hormones that boost immunity and decrease inflammation [11].

Also, as mentioned above, after the water breaks, exposure to vaginal flora begins. One study found that babies born from a C-section tended to have lower levels of Escherichia-Shigella and Bacteroides species compared to those born through labor. 

The study noted these differences were more apparent in women who elected for a C-section rather than a woman who started going into labor and had to get an emergency procedure [12]. These findings further prove that the labor process already introduces vaginal flora to the baby.

Are Antibiotics More Harmful Than C-Sections?

In many cases, antibiotics are a lifesaving necessity during birth, but that does not mean they don’t have their drawbacks. It is already common knowledge that antibiotics can harm your gut microbiome [13]. Even scarier, studies show that they can have negative implications for babies before they are even born. 

One analysis published through the National Institutes of Health found,

“Our results indicate an effect of IAP (intrapartum antimicrobial prophylaxis) on the establishing early microbiota during the first months of life, which represent a key moment for the development of the microbiota-induced host homeostasis [14].”
- Microbiome
Some studies show that it may not be the actual C-section that causes the differences in microbiome and disease development in children, but the antibiotics are to blame [15]. 

Antibiotics During C-Sections

When C-sections are performed, antibiotics are given during or after surgery to prevent infection. The problem is, different antibiotic protocols are used during C-section deliveries. Sometimes they are administered during or after the surgery. 

Also, sometimes antibiotics are administered during vaginal deliveries, such as when a woman has Group B strep [16].

Not shockingly, babies born vaginally that are exposed to antibiotics show similar microbial results to babies born via C-section who were exposed to antibiotics [17]. 

Their gut microbiome is more susceptible to pathogens, which can cause immune responses more frequently. That’s because antibiotics wipe out all bacteria.

If your doctor ever recommends you take antibiotics during the birthing process, you need to take them. Often antibiotics can be a lifesaving tool for both mom and baby. 

This lifesaving measure does not mean they don’t come with drawbacks, though. It is good to talk to your doctor about minimizing unnecessary antibiotic use before the birthing process begins.

Breastfeeding for Baby Health

Research suggests babies that are breastfed are generally healthier later in life. It is rich in protein that promotes growth, colostrum that supports a healthy immune system, and lactic acid that improves digestion. That’s why the American Academy of Pediatrics highly recommends this act.

They state,

“The American Academy of Pediatrics reaffirms its recommendation of exclusive breastfeeding for about 6 months, followed by continued breastfeeding as complementary foods are introduced, with continuation of breastfeeding for 1 year or longer as mutually desired by mother and infant [17].”
– American Academy of Pediatrics

Another critical component of microbiome development is whether or not a baby was breastfed. Recent scientific discoveries found that breast milk contains many probiotic bacteria and prebiotics that help to develop a healthy microbiome [18].

Breast Milk Probiotics and Baby Growth

Often babies born via C-section have a more challenging time breastfeeding and do not breastfeed as frequently or as long [19]. This difference is another factor that could account for the correlations between C-section delivery and disease development later on. 

When you breastfeed, it’s essential to keep with a regular schedule. As your baby gets older, the breast milk changes in composition to continually meet the baby's nutritional needs [20]. 

Vaginal Seeding for Newborns

Seeding is when a baby born by C-section is exposed to vaginal fluids immediately after birth. This practice is done by swabbing the baby in gauze with vaginal fluids from the mother to “seed” the baby’s microbiome [21]. 

The rationale behind seeding is that all of the negative correlations associated with C-sections are because the baby is not exposed to the bacteria-rich vaginal fluids. While a thoughtful theory, there are some concerns and further research is needed. We need a better understanding before we can endorse such a process. 

Additionally, the American College of Obstetrics and Gynecologists does not recommend this practice since it can introduce pathogens and harmful bacteria into the baby’s environment. 

There are instances where babies can become ill due to pathogenic bacteria in the vagina. Therefore, the risks do not outweigh the costs with the current research [22]. 

Are C-Sections Dangerous for Baby Gut Health?

There is a correlation between a multitude of diseases later in life and C-section delivery. Right now, we don’t know exactly how much of that is due to microbial changes due to the type of childbirth.

Even if you need to have a C-section, all hope is not lost; you can still give your baby the best shot at having a healthy microbiome. Being educated on all the different ways your baby’s microbiome can be affected is essential. It’s good to realize the story is not entirely so black and white, and shades of gray are okay!


[1] Luxembourg, University of. “Altered Microbiome after Caesarean Section Impacts Baby's Immune System.” ScienceDaily, ScienceDaily, 30 Nov. 2018, www.sciencedaily.com/releases/2018/11/181130094328.htm.

[2] Neu, J., & Rushing, J. (2011). Cesarean versus vaginal delivery: long-term infant outcomes and the hygiene hypothesis. Clinics in perinatology, 38(2), 321–331. doi:10.1016/j.clp.2011.03.008

[3] Kero, Jukka, et al. “Mode of Delivery and Asthma -- Is There a Connection?” Pediatric Research, U.S. National Library of Medicine, July 2002, www.ncbi.nlm.nih.gov/pubmed/12084840.

[4] Algert, C S, et al. “Perinatal Risk Factors for Early Onset of Type 1 Diabetes in a 2000-2005 Birth Cohort.” Diabetic Medicine : a Journal of the British Diabetic Association, Blackwell Publishing Ltd, Dec. 2009, www.ncbi.nlm.nih.gov/pubmed/20002469.

[5] Decker, Evalotte, et al. “Cesarean Delivery Is Associated with Celiac Disease but Not Inflammatory Bowel Disease in Children.” Pediatrics, U.S. National Library of Medicine, June 2010, www.ncbi.nlm.nih.gov/pubmed/20478942.

[6] Ajslev, T A, et al. “Childhood Overweight after Establishment of the Gut Microbiota: the Role of Delivery Mode, Pre-Pregnancy Weight and Early Administration of Antibiotics.” International Journal of Obesity (2005), U.S. National Library of Medicine, Apr. 2011, www.ncbi.nlm.nih.gov/pubmed/21386800.

[7] Collado, Maria Carmen, et al. “Human Gut Colonisation May Be Initiated in Utero by Distinct Microbial Communities in the Placenta and Amniotic Fluid.” Nature News, Nature Publishing Group, 22 Mar. 2016, www.nature.com/articles/srep23129.

[8] Wall, R., Ross, R. P., Ryan, C. A., Hussey, S., Murphy, B., Fitzgerald, G. F., & Stanton, C. (2009). Role of gut microbiota in early infant development. Clinical medicine. Pediatrics, 3, 45–54. https://doi.org/10.4137/cmped.s2008.

[9] Stinson, Lisa F., et al. “A Critical Review of the Bacterial Baptism Hypothesis and the Impact of Cesarean Delivery on the Infant Microbiome.” Frontiers, Frontiers, 20 Apr. 2018, www.frontiersin.org/articles/10.3389/fmed.2018.00135/full.

[10] “Labor and Childbirth: What To Expect & Complications.” WebMD, WebMD, www.webmd.com/baby/guide/normal-labor-and-delivery-process.

[11] Malamitsi-Puchner, Ariadne, et al. “The Influence of the Mode of Delivery on Circulating Cytokine Concentrations in the Perinatal Period.” Early Human Development, U.S. National Library of Medicine, Apr. 2005, www.ncbi.nlm.nih.gov/pubmed/15814224.

[12] Azad, Meghan B, et al. “Gut Microbiota of Healthy Canadian Infants: Profiles by Mode of Delivery and Infant Diet at 4 Months.” CMAJ : Canadian Medical Association Journal = Journal De L'Association Medicale Canadienne, Canadian Medical Association, 19 Mar. 2013, www.ncbi.nlm.nih.gov/pubmed/23401405.

[13] Langdon, A., Crook, N., & Dantas, G. (2016). The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome medicine, 8(1), 39. doi:10.1186/s13073-016-0294-z

[14] Nogacka, Alicja, et al. “Impact of Intrapartum Antimicrobial Prophylaxis upon the Intestinal Microbiota and the Prevalence of Antibiotic Resistance Genes in Vaginally Delivered Full-Term Neonates.” Microbiome, BioMed Central, 8 Aug. 2017, www.ncbi.nlm.nih.gov/pubmed/28789705.

[15] Azad, MB, et al. “OBGYN.” Obstetrics and Gynecology, John Wiley & Sons, Ltd (10.1111), 28 Sept. 2015, obgyn.onlinelibrary.wiley.com/doi/full/10.1111/1471-0528.13601.

[16] Aloisio, Irene, et al. “Influence of Intrapartum Antibiotic Prophylaxis against Group B Streptococcus on the Early Newborn Gut Composition and Evaluation of the Anti- Streptococcus Activity of Bifidobacterium Strains.” SpringerLink, Springer Berlin Heidelberg, 1 Apr. 2014, link.springer.com/article/10.1007%2Fs00253-014-5712-9.

[17] Breastfeeding, Section On. “Breastfeeding and the Use of Human Milk.” Pediatrics, American Academy of Pediatrics, 1 Mar. 2012, pediatrics.aappublications.org/content/129/3/e827.

[18] Rautava, S. “Early Microbial Contact, the Breast Milk Microbiome and Child Health.” Journal of Developmental Origins of Health and Disease, U.S. National Library of Medicine, Feb. 2016, www.ncbi.nlm.nih.gov/pubmed/26051698.

[19] Bai, Dorothy Li, et al. “Association between Intrapartum Interventions and Breastfeeding Duration.” Journal of Midwifery & Women's Health, U.S. National Library of Medicine, 2013, www.ncbi.nlm.nih.gov/pubmed/23317341.

[20] Ballard, O., & Morrow, A. L. (2013). Human milk composition: nutrients and bioactive factors. Pediatric clinics of North America, 60(1), 49–74. doi:10.1016/j.pcl.2012.10.002

[21] “Women's Health Care Physicians.” ACOG, www.acog.org/Clinical-Guidance-and-Publications/Committee-Opinions/Committee-on-Obstetric-Practice/Vaginal-Seeding?IsMobileSet=false.

[22] Embleton, Nick, et al. “Mortality from Early Onset Group B Streptococcal Infection in the United Kingdom.” ADC Fetal & Neonatal Edition, BMJ Publishing Group, 1 Mar. 1999, fn.bmj.com/content/80/2/F139.


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