Vaginal Microbiome and C-Sections: Does Delivery Effect Baby’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. When the baby passes through the vaginal microbiome, your incoming bundle of joy gets exposed to a plethora of bacteria [1].

Common idea is that this initial exposure of the baby to the vaginal microbiome is pivotal in setting the trajectory for the baby’s health. This belief system is known as the hygiene hypothesis. While there is some credibility to the hygiene hypothesis, it doesn’t mean a baby born via C-section is doomed.

Many interchanging variables may give C-sections a wrongful negative stigma. Let’s learn more about the vaginal microbiome and how C-sections may affect your baby’s gut health.

Vaginal Delivery vs. C-Section

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. Therefore, your baby’s health may be just fine. In fact, some C-sections still expose your baby to healthy stomach bacteria!

Misconceptions About C-Sections

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

C-Sections are generally safe but there are elevated risks that seem to be associated

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. Not only do each mother have their own set of immune cells that they transfer to their children, but each individual C-section is performed under different circumstances.

All of these subtle differences in pregnancies make each experience special.

Vaginal Microbiome and Pre-Birth Microbial Exposure

Babies do not live in a sterile environment like we once thought. Bacteria are found throughout the womb. Not to mention, there are stomach 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] .”


These findings show that a baby’s exposure to bacteria happens before it 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 stomach bacteria in the vaginal microbiome. 

vaginal microbiome
There are many microbes
in amniotic fluids

Even if the result of the birth is a C-section, the broken amniotic sac allows some bacterial exposure from the vaginal microbiome.

This partial greeting between fetus and microbes affects the baby’s microbiome.

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 [8].

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 [9].

When these changes happen, it causes:

vaginal microbiome
Thank goodness I’m out!
  • 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 [10].

Also, as mentioned above, after the water breaks, vaginal bacteria exposure begins. One study found that babies that were born after the mother labored had a different microbiome than if the mother hadn’t [11].

Labor makes a difference in the initial development and health of a newborn. Many women who have C-sections undergo the procedure long after the labor process has begun. Some women, however, go through the C-section process before labor has started.

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 microbiome [12]. Even scarier, studies are showing that they can affect babies before they are even born. 

One analysis 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 [13].”


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 [14]. 

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. 

baby just born
So many things are out of our control
before we enter this world

Also, sometimes antibiotics are administered during vaginal deliveries, such as when a woman has Group B strep [15].

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 [16].  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 life-saving 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. 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 [16].”

American Academy of Pediatrics

Another critical component of microbiome development is whether or not a baby was breastfed. Breastmilk has been found to contain many probiotic bacteria and prebiotics that help to develop a healthy microbiome [17].

Breastmilk Probiotics and Baby Growth

Often babies who were born via C-section have a harder time breastfeeding and do not breastfeed as frequently or as long [18]. This difference is another factor that could account for the correlations between C-section delivery and disease development later on. 

breast milk immune cells
Learn More: Probiotics in Breast Milk

When you breastfeed, it’s important to keep with a regular schedule. As your baby gets older, the breast milk changes in composition to continually meet the nutritional needs of the baby [19]. 

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 [20]. 

new born baby in incubator
Vaginal seeding is a controversial new practice for introducing mother’s microbes to baby

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 is no reliable evidence that the initial vaginal microbiome exposure determines the trajectory of the baby’s microbiome.

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 [21]. 

Is 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 what component of delivery or after-birth care makes the most significant difference. 

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 sometimes those shades of gray are okay!

Thryve Probiotics Gut Health


[1] Luxembourg, University of. “Altered Microbiome after Caesarean Section Impacts Baby’s Immune System.” ScienceDaily, ScienceDaily, 30 Nov. 2018,

[2] Neu, J., & Rushing, J. (2011). Cesarean versus vaginal delivery: long-term infant outcomes and the hygiene hypothesis. Clinics in perinatology38(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,

[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,

[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,

[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,

[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,

[8] 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,

[9] “Labor and Childbirth: What To Expect & Complications.” WebMD, WebMD,

[10] 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,

[11] 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,

[12] Langdon, A., Crook, N., & Dantas, G. (2016). The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome medicine8(1), 39. doi:10.1186/s13073-016-0294-z

[13] 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,

[14] Azad, MB, et al. “OBGYN.” Obstetrics and Gynecology, John Wiley & Sons, Ltd (10.1111), 28 Sept. 2015,

[15] 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,

[16] Breastfeeding, Section On. “Breastfeeding and the Use of Human Milk.” Pediatrics, American Academy of Pediatrics, 1 Mar. 2012,

[17] 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,

[18] 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,

[19] Ballard, O., & Morrow, A. L. (2013). Human milk composition: nutrients and bioactive factors. Pediatric clinics of North America60(1), 49–74. doi:10.1016/j.pcl.2012.10.002

[20] “Women’s Health Care Physicians.” ACOG,

[21] 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,