# What Forms the Newborn's Microbiome After Birth The newborn's microbiome is shaped by several key
The arrival of new life into the world is a moment full of emotions, but also a fascinating biological process that shapes a child's health for many years to come. One aspect that science has been studying with increasing intensity in recent decades is the newborn's microbiome – the collection of billions of bacteria, viruses and fungi that colonise its body immediately after birth. And the mode of delivery, whether vaginal or caesarean section, plays a surprisingly fundamental role in this process.
The human microbiome generally consists of approximately 38 trillion microorganisms, their number roughly equalling the number of the body's own cells. This finding, published in 2016 by a team of scientists in the journal Cell, fundamentally changed the perspective on what we actually "are". A newborn comes into the world practically as a blank slate – its intestines, skin and mucous membranes are yet to be colonised. And what colonises them first may determine its immunity, susceptibility to allergies and metabolic health for its entire life.
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Vaginal birth as a natural bacterial initiation
During passage through the birth canal, something occurs that can be compared to a biological baptism. The newborn comes into contact with the mother's vaginal microflora, which is rich primarily in bacteria of the Lactobacillus genus. These microorganisms are crucial for the development of a healthy intestinal environment – they help digest the first milk, protect against pathogens and actively stimulate the development of the immune system.
Let us illustrate this with a specific example: little Eliška is born vaginally at 39 weeks of pregnancy. Within a few hours of birth, her intestines begin to be colonised by bacteria she received directly from her mother. These bacteria initiate the fermentation of breast milk, produce short-chain fatty acids and create the first line of defence against potentially harmful microorganisms from the surrounding environment. Her microbiome is diverse and functional from the very first day.
Research shows that vaginally born children have a microbiome that, in the first months of life, closely resembles that of the mother. According to a study published in the prestigious scientific journal Nature Medicine in 2019, these children have significantly higher levels of beneficial bacteria such as Lactobacillus, Bacteroides and Bifidobacterium, with Bifidobacterium in particular considered a key player in the healthy development of the infant gut.
This natural transfer of microorganisms is not random – evolution has refined it over millions of years so that the newborn receives precisely the bacteria it needs for its start in life. It is therefore no surprise that deviations from this process have measurable consequences.
Caesarean section and its effect on the newborn's microbiome
Caesarean section is in many cases necessary and saves the lives of both mothers and children. No one should be denied this option or have it trivialised. Nevertheless, it is important to speak openly about the fact that the mode of delivery has biological consequences that deserve attention.
Children born by caesarean section do not pass through the birth canal, and therefore do not come into contact with the mother's vaginal microflora. Instead, their first microbial contacts come from the mother's skin, the hands of medical staff and the hospital environment. The resulting microbiome is therefore composed predominantly of bacteria typical of the hospital environment – such as Staphylococcus, Streptococcus and Clostridium – rather than beneficial lactobacilli.
The difference in intestinal microbial composition between children born vaginally and by caesarean section is evident throughout the first months and sometimes even years of life. A study from 2020, published in Cell Host & Microbe, followed the microbiome of more than 600 children and confirmed that children born by caesarean section have significantly lower diversity of intestinal microbiome in the first year of life. This reduced diversity correlates with a higher risk of developing allergies, asthma, eczema, as well as obesity and type 2 diabetes in later life.
As leading British microbiologist Tim Spector described it in his book The Diet Myth: "The way we come into the world shapes our health in ways we are only beginning to understand."
This finding does not mean that every child born by caesarean section will be ill – health is the result of many factors. However, awareness of these connections opens up space for interventions that can help support the newborn's microbiome.
Microbiome seeding – a controversial but interesting practice
In recent years, the practice known as "vaginal seeding" or microbial inoculation has been discussed in professional circles. This is a procedure in which a cotton swab saturated with the mother's vaginal secretion is applied to the skin, mouth and nose of the newborn immediately after caesarean section. The aim is to mimic the natural transfer of bacteria during vaginal birth.
A pilot study published in Nature Medicine in 2016 suggested that this procedure does indeed help bring the microbiome of a caesarean-born child closer to that of a naturally born child. At the same time, however, professional societies, including the American College of Obstetricians and Gynecologists, point out that the procedure carries risks of transmitting pathogens such as herpes simplex virus, and do not recommend it as standard practice without prior testing of the mother.
Research in this area is ongoing and consensus has not yet been reached. Nevertheless, it is an example of how science is actively seeking ways to equalise the differences arising from the mode of delivery.
Breastfeeding as a second chance for the microbiome
Regardless of the mode of delivery, there is one factor that has a fundamental influence on the newborn's microbiome and is available to almost every mother – breastfeeding. Breast milk is not merely a source of nutrients. It contains special oligosaccharides (HMOs – human milk oligosaccharides) that are not intended for the child itself, but directly for its intestinal bacteria. These substances selectively promote the growth of Bifidobacterium and other beneficial microorganisms.
Research repeatedly shows that breastfed children have a healthier and more diverse intestinal microbiome than formula-fed children, regardless of the mode of delivery. A study from JAMA Pediatrics demonstrated that breastfeeding can partially compensate for the microbial deficit arising from caesarean section. In children born by caesarean section who were breastfed for at least six months, the difference in microbiome compared to vaginally born children was significantly smaller than in formula-fed children.
This is a message that should be part of every conversation about postnatal care. Mothers who gave birth by caesarean section can pass on a microbial legacy to their child through breastfeeding that would otherwise come through the natural route.
Another factor that shapes the newborn's microbiome is contact with nature and the home environment. Children growing up in households with animals, who spend time outdoors and are in contact with soil, demonstrably have a more diverse microbiome than children growing up in strictly sterile environments. This insight stems from the so-called hygiene hypothesis, according to which the excessive sterility of the modern environment deprives the immune system of necessary stimuli and contributes to the rise in allergies and autoimmune diseases.
Parents who are interested in supporting their child's healthy microbiome can also turn to probiotic dietary supplements specifically designed for infants. Products containing strains of Lactobacillus rhamnosus or Bifidobacterium longum are available on the market, and their effectiveness in supporting intestinal health in infants is confirmed by a number of clinical studies. However, it is always advisable to consult a paediatrician before using them.
It is also important to remember that the microbiome is not a static matter. Even though the first months of life are crucial for its formation, the intestinal ecosystem develops and changes throughout life. A diet rich in fibre, fermented foods, limiting unnecessary use of antibiotics and spending time in nature are factors that can positively influence the microbiome at any age.
What science says about long-term impacts
Epidemiological data are fairly unambiguous in this regard. The global rise in caesarean section births – in some countries now accounting for over 50% of all births – correlates temporally with the rise in the incidence of allergies, asthma, coeliac disease, inflammatory bowel diseases and autoimmune disorders. Direct causality is difficult to prove, as health is influenced by dozens of variables, but the associations are strong enough that the scientific community takes them seriously.
The World Health Organization in its statement warns that a caesarean section rate above 10–15% of the population no longer brings measurable benefits for the health of mothers or children and may be associated with negative consequences. This does not mean that caesarean sections should not be performed where medically indicated – quite the contrary. But there is growing pressure to ensure that this operation is not performed unnecessarily merely for convenience or out of fear of pain, without parents being informed of all the potential consequences.
Informed decision-making is key. Parents who know how the mode of delivery affects the newborn's microbiome can better plan postnatal care – whether it concerns breastfeeding, probiotics, contact with nature or regular monitoring of the child's health. Science in this area is advancing rapidly and each year brings new findings that help us better understand how fragile and yet fascinating the start of every new life in this world truly is.
