C-Section vs Natural Birth Microbiome

C-Section vs Natural Birth Microbiome: How The First Bacteria We Meet Can Influence Our Health

18 June 2025

An adult hand reaching out to a newborn baby's hand

In this article, we’ll look at how the way a baby is born, either through vaginal delivery or caesarean section, can influence the development of their gut microbiome. We’ll explore the main differences in the types of bacteria babies are first exposed to during birth and how this may affect their health, both in the short and long term.

We’ll also look at whether babies born by C-section have a different gut microbiome from those born vaginally, and what this might mean for their immune system and risk of certain conditions.

As well as looking at current research, we’ll also discuss where future research is heading, and how scientists are working to better understand the importance of bacteria from birth.

Key Takeaways

Here are the five biggest takeaways from this article regarding how the mode of birth can influence gut microbiome:

The way a baby is born, be it vaginally or via caesarean section, significantly affects their first exposure to bacteria.
Vaginal births introduce babies to beneficial bacteria from the mother’s vaginal and gut microbiota, which helps establish a healthy and diverse gut microbiome.
Babies born by C-section are typically colonised by bacteria from the skin and hospital environment rather than the mother’s birth canal.
Breastfeeding, skin-to-skin contact, diet and other factors can help improve the balance of gut bacteria in babies born by C-section.
Some studies suggest that while there are differences in early microbial exposure between vaginal and C-section births, these may not lead to lasting health effects.

How does a natural birth (vaginal delivery) affect a baby's microbiome?

A natural birth (vaginal delivery) plays an important role in shaping a baby’s microbiome (the collection of bacteria and other microorganisms that live in and on the body). During a vaginal birth, the baby passes through the birth canal and is exposed to the mother’s vaginal and gut bacteria. These are some of the first microbes to colonise the baby’s skin, mouth and gut.

This early exposure helps to start the development of the baby’s immune system and supports the growth of a balanced gut microbiome. Bacteria picked up during birth can influence how the baby’s body responds to infections, inflammation and even how they digest food. It is thought that babies born vaginally are more likely to develop a diverse range of gut bacteria early on, which may help to protect against allergies, asthma and obesity later in life.

It’s important to note that other factors, such as breastfeeding, genetics, environment and antibiotic use, also play a role in shaping the microbiome as the baby grows. Despite this, the method of delivery is one of the first and most significant steps in this process.

How does a C-section birth affect a baby's microbiome?

A caesarean section (also known as a C-section) birth can affect a baby’s microbiome differently to a vaginal delivery. Because the baby does not pass through the birth canal, they are not exposed to the same bacteria from the mother’s vagina and gut. Instead, babies delivered via C-section are more likely to be colonised by bacteria from the skin, the hospital environment and the people who handle them after birth. As a result, their gut microbiome may take longer to develop and may contain fewer types of beneficial bacteria in the early weeks of life.

This difference in early bacterial exposure has been linked to a slightly higher risk of developing certain health conditions later on, such as:

Asthma
Eczema
Allergies
Obesity

It’s important to remember, however, that a baby’s microbiome is not fixed at birth. It continues to evolve over time, and factors like breastfeeding, diet and environment can all help to support a healthy balance of gut bacteria.

Do cesarean-born babies have a different gut microbiome than naturally born babies?

Yes, babies born by C-section do tend to have a different gut microbiome compared to those born through vaginal delivery. The way a baby is born plays a key role in determining the types of bacteria that first colonise their gut.

Children delivered vaginally are typically exposed to bacteria from the mother’s birth canal, including Lactobacillus and Bifidobacterium species. These are considered beneficial for developing a balanced and healthy gut microbiome [1]. On the other hand, babies born via C-section are more often colonised by microbes from the skin, hospital surfaces and people they come into contact with. This can lead to a different bacterial composition in the early stages of life [2].

Several studies have confirmed that the microbiome of C-section born infants is less diverse and shows delayed development compared to those delivered vaginally [3] [4]. This can last for months and in some cases, even up to a year. These differences have been linked to a higher risk of immune-related conditions, such as asthma, allergies, type 1 diabetes and obesity later in life [5] [6].

Research also shows that the gut microbiota in C-section babies often has lower levels of Bacteroides and Bifidobacterium, and higher levels of opportunistic pathogens. These are thought to influence how the immune system matures, particularly during the critical early period after birth [7] [8].

Scientists are actively studying ways to help support the microbiome in babies born by C-section. These include promoting breastfeeding, delaying bathing after birth and exploring the use of probiotics or vaginal seeding, the process of exposing a newborn baby to the mothers vaginal fluids.

While C-section births can result in a different and sometimes less beneficial gut microbiome early on, the microbiome is not fixed. With the right support, many of these differences can be reduced over time.

Contrasting Views

While many studies suggest clear differences in the gut microbiome between babies born via caesarean section and those born vaginally, some researchers argue that these differences may not be as long-lasting or as significant as previously thought.

According to research from the University of Edinburgh, babies receive essential microbes from their mothers regardless of how they are born. The study found that while the first bacterial exposure may differ between vaginal and C-section deliveries, these early differences may not lead to long-term health implications. It suggests that the maternal microbiome continues to influence the baby’s gut in other ways, such as breastfeeding and skin-to-skin contact, which can help balance any initial differences [9].

A separate study led by UCL also supports this view. It states that although babies born by C-section may have some variation in their early microbiome, these differences often disappear by the time the child is one year old. This research challenges the idea that delivery method has a lasting impact on the microbiome, suggesting instead that the microbiome is highly adaptable when a baby is young. It also points out that both groups can develop a microbiome capable of supporting a healthy immune system [10].

Where is the current and future research in this area focusing?

Current and future research in this area is focusing on better understanding how to support the development of a healthy microbiome in all babies, regardless of how they are born. While it is clear that the mode of delivery can influence a baby’s early microbiome, scientists are looking at ways to reduce any potential long-term impact, particularly for babies born by C-section.

One area of growing interest is vaginal microbiota transfer (VMT). This involves swabbing a C-section baby with the mother’s vaginal fluids shortly after birth to expose the baby to the same types of bacteria they would have encountered during a vaginal delivery. Early studies suggest that VMT may help to partially restore the microbiome in C-section babies, although more research is needed to confirm its safety and effectiveness before it can be widely recommended.

Research is also examining how breastfeeding, skin-to-skin contact and timing of antibiotic use can influence the gut microbiome in babies. These factors may help to support a more balanced and diverse microbiome, particularly in babies who do not experience the same bacterial exposure at birth.

Final Thoughts From Yusra

While the mode of birth can influence a baby’s early exposure to bacteria and the development of their gut microbiome, this is just one factor. Babies born vaginally tend to receive more beneficial microbes at birth, while those born by C-section may develop a different microbial balance in the early weeks.

However, the microbiome continues to evolve and can be supported through factors such as breastfeeding, skin-to-skin contact and overall care. Some research suggests these early differences may affect long-term health, while others argue the microbiome often evens out within the first year of life.

As research continues, the focus is on finding safe, effective ways to support healthy microbial development for all babies, regardless of how they are born.

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