Mya Care Blogger 06 May 2024

Disclaimer: While this article aims to provide the latest information and insights, please note that there are many instances where C-sections may be necessary to save lives. We reiterate that the health and safety of the mother and baby take top priority. Therefore, it is advisable to discuss your questions with a maternal fetal specialist.

When it comes to giving birth, there are two main delivery methods: vaginal birth and cesarean section. While both methods have benefits and risks, one aspect often overlooked is the impact on the newborn’s microbiome.

The microbiome is a collective of microbes that live in and on our bodies, including bacteria, viruses, and fungi. We rely on these microbes for a large portion of our overall health, from digestion and immunity to brain development.

This blog reviews the effect of delivery mode on the baby's gut bacteria and the potential consequences.

Why is the Baby's Microbiome Important?

The microbiome is essential for three main reasons: digestion, immunity, and brain neurodevelopment.

Digestion: The gut microbiome enables the breakdown of food and nutrient absorption. In infants, it provides the premature digestive system with enough energy to sustain rapid growth and development.[1]

A diverse gut microbiome is fundamental for proper digestion and can help deter issues like constipation and diarrhea.

Immunity: The gut microbiome also plays a significant role in the development of the immune system.[2]

A diverse microbiome helps train the immune system to determine and fight off harmful bacteria and viruses. It also shapes its responses to allergens. Another way a robust infantile microbiome enhances child immunity is by interacting with immune cells in the gut to control immune responses directly.

These mechanisms contribute to the establishment of a healthy and resilient immune system, protecting infants from infections and allergies.

Brain Development: The infant gut microbiome[3] produces short-chain fatty acids (SCFAs) essential for brain growth and function and neuroactive compounds directly affecting brain function. SCFAs also impact the immune system, indirectly affecting brain development.

The microbiome also influences the gut-brain axis, a communication system between the gut and the brain. This axis allows for bidirectional signaling and regulation of brain functions with the gut.

Vaginal vs. Cesarean Delivery

Microbiome transfer from mother to baby is essential for developing a diverse and healthy microbiome. As explained, a healthy microbiome is critical for optimal development.

In recent years, researchers have begun to unravel the impact of vaginal delivery and cesarean delivery on the infantile microbiome. The difference is astounding.

Vaginal delivery

Babies born vaginally enter the world with a richer and more diverse microbiome than C-section babies. The vaginal microbiome contains a wealth of beneficial bacteria, such as Lactobacillus species. These bacteria help to protect the baby from harmful bacteria and promote the development of a healthy immune system.

Vaginal delivery lessens the infant’s lifelong risk of developing specific health ailments, such as allergies, asthma, obesity, and autoimmune diseases[4]. These protective benefits likely arise from the exposure to the rich and diverse microbiome of the birth canal.

Cesarean delivery (C-section)

Babies born by C-section begin their lives with a different microbiome than babies born vaginally. The skin microbiome of the mother is the primary source of bacteria for C-section babies. This microbiome is less diverse and contains fewer beneficial bacteria than the vaginal microbiome.

By contrast to traditional gut bacteria, skin bacteria use sparse nutrients found on the surface of the skin.[5] If skin bacteria populate the gut, it may impact nutrient availability, production, and absorption that would otherwise spur infantile growth.

As a result of lower microbiome diversity, studies show that babies born by C-section have an elevated risk of developing certain health conditions, such as allergies, asthma, obesity, and autoimmune diseases.

Vaginal birth transfers the mother's microbiome to the baby, which helps to "seed" the infant's microbiome and set it off to a better start.

Researchers believe that vaginal seeding helps to regulate the infant's metabolism from earlier on in life than without, minimizing the vulnerability of the infant during this critical phase of life.

Studies associated vaginal microbiota transfer with a lower risk of various health conditions later in life, including:

Infants inoculated with their mother's vaginal microbiome also experience improved health outcomes on average, including fewer respiratory infections and hospital readmissions.

While interesting, more research is required to verify the above findings.

Maternal Microbiota and Miscarriage Risk

Studies indicate a connection between the diverse community of microbes in the vagina and a healthy pregnancy. Balanced bacterial communities may promote a receptive environment for fetal implantation, while imbalances might increase inflammation or disrupt immune regulation, potentially leading to miscarriage[6]. Research also suggests that the gut microbiome, which can influence the vaginal microbiome, might play a role. However, more research is needed to fully understand the specific cause-and-effect relationships and identify potential interventions.

Cesarean-related Influences on the Microbiome

Cesarean delivery (C-section) bypasses the natural passage of the birth canal, depriving the infant of the beneficial bacteria present in the mother's vaginal microbiome.[7]

A lower-diversity microbiome is associated with several potential negative consequences for infant health and development, including:

  • Increased risk of allergies: Lower microbiome diversity may contribute to an overactive immune system, making infants more susceptible to allergies.
  • Delayed gut maturation: C-section babies may experience delayed gut maturation, affecting digestion and nutrient absorption. It may also increase the risk of colic.
  • Altered immune system development: A less diverse microbiome may provide a different level of immune system training and reactivity, potentially raising autoimmune disease risk later in life.
  • Cognitive development: Emerging research suggests that a lower-diversity microbiome can also impact cognitive development, potentially affecting learning, memory, and attention. Infants without complete diversity may lack vital gut-derived neuroactive peptides and SCFAs needed for brain development.

C-Section Antibiotic Use

Another potential issue of C-section birth is the administration of antibiotics before the operation. Some studies have traced the adverse effects of cesarean birthing to the antibiotics administered and not necessarily to a lack of exposure to the mother's vaginal microbiome.

Vaginal Seeding Research and Controversy

In recent years, there has been a growing trend of "vaginal seeding" for babies born via cesarean section.

While some studies have shown potential benefits of vaginal seeding, the evidence is limited, and the practice is advised against by the American College of Obstetricians and Gynaecologists.[8]

Some studies contradict all beneficial findings related to vaginal seeding, stating that there are no infantile microbiome differences between delivery methods, that the differences clear up within 3-6 months, or that the practice is ineffective. Other findings suggest that the expansion of the vaginal canal may expose the infant to rectal bacteria and that this might contribute more benefit than the vaginal microbiome.

There are also concerns about the potential transfer of harmful bacteria and the lack of long-term trials assessing the safety and efficacy of vaginal seeding.

These results suggest that infantile microbiome development is a complicated process that can be affected by multiple exposures. More research can help to establish firm conclusions about the topic.

Post-Cesarean Microbiome Support

While vaginal seeding may improve outcomes, there are other ways to support the baby's microbiome after a cesarean section. These include[9]:

  • Skin-to-skin contact after birth helps transfer beneficial bacteria from mother to baby
  • Probiotics for the mother can promote a diverse microbiome
  • Breastfeeding nourishes the baby's gut bacteria with beneficial bacteria and prebiotics. Studies suggest this lowers the risk of colic

These practices are likely beneficial for all mothers, irrespective of delivery mode.

While these interventions show promise, more research is needed to determine their long-term effects and identify the most effective methods.

Infantile Fecal Microbiota Transplant

Researchers are also evaluating whether fecal microbiota transplant (FMT) from mother to infant poses benefits.

A limited study reveals that C-section babies treated with FMT displayed a microbiome similar to vaginally delivered babies. More studies are needed to confirm these results and to understand potential side effects, such as potential disease transmission and other long-term health consequences.

Holistic Approach to Baby Health

While the delivery mode can impact the baby's microbiome, it is not the only factor. A holistic approach to baby health is essential for developing a healthy microbiome.

Some tips for holistically enhancing a baby's microbiome are:

  • Delay the first bath: Your baby will have vernix on their skin after birth. It helps regulate their temperature, has antioxidants, and moisturizes the skin. It also contains bacteria from the mother's vaginal flora after vaginal delivery. Rub it in gently and postpone bathing for a week for maximum benefits.[10]
  • Nurture your baby: A nurturing and loving environment can lower stress, facilitating a healthier microbiome.
  • Introduce solid foods gradually: A diverse range of foods, including prebiotic-rich foods, can help promote a diverse microbiome. However, introducing solid foods too early can disrupt the balance of the infant's microbiome. Experts advise introducing solid foods gradually, starting with a few single-ingredient foods.
  • Bypass antibiotics: Antibiotics can unsettle the balance of the microbiome by killing both beneficial and harmful bacteria. Only use antibiotics when necessary, and follow your doctor's instructions carefully.
  • Support a healthy home environment: Creating a healthy environment for the infant that includes regular exercise and exposure to nature contributes to a healthier overall microbiome. Excessive cleanliness can also disrupt the balance of the microbiome. Minimize the usage of harsh cleaning detergents and air fresheners around the infant.
  • Introduce pets cautiously: Studies show that exposure to pets can improve the diversity of the infant's microbiome. However, it is advisable to introduce pets cautiously, especially if allergies or asthma are a concern.

Talk to a professional pediatrician if you have concerns about your infant's microbiome health. An expert can offer personalized recommendations based on your baby’s needs.


The delivery mode can significantly impact the baby's microbiome, which can have long-term consequences for the baby's health. While vaginal birth is ideal for the transfer of the mother's beneficial microbiome, there are ways to support the baby's microbiome after a cesarean section. A holistic approach to baby health, including diet, environment exposure, and a nurturing environment, is essential for developing a diverse and healthy microbiome. It is also worth noting that while natural childbirth is known to expose babies to beneficial gut bacteria, a cesarean section may sometimes be the only viable option to ensure the safety and health of both mother and baby, which takes precedence over concerns about initial microbial colonization.

To search for the best Obstetrics and Gynecology healthcare providers in Germany, India, Malaysia, Poland, Saudi Arabia, Singapore, Slovakia, Spain, Thailand, Turkey, the UAE, the UK and the USA, please use the Mya Care search engine.

To search for the best doctors and healthcare providers worldwide, please use the Mya Care search engine.


  • [1]
  • [2]
  • [3]
  • [4]
  • [5]
  • [6]
  • [7]
  • [8]
  • [9]
  • [10]

Disclaimer: Please note that Mya Care does not provide medical advice, diagnosis, or treatment. The information provided is not intended to replace the care or advice of a qualified health care professional. The views expressed are personal views of the author and do not necessarily reflect the opinion of Mya Care. Always consult your doctor for all diagnoses, treatments, and cures for any diseases or conditions, as well as before changing your health care regimen. Do not reproduce, copy, reformat, publish, distribute, upload, post, transmit, transfer in any manner or sell any of the materials in this blog without prior written permission from