At birth, the bacterial world invites itself into the newborn's body like a crucial but invisible guest. This pivotal moment, often summed up as a simple cry or a weight on the scale, nevertheless marks the silent beginning of a fundamental process. Because from the first hours, the infant's intestinal microbiota begins to take hold, gradually drawing the contours of a future health that is still unknown.
The precise moment when everything begins to play out
The infant is born sterile, or almost. Deprived of bacteria in the uterus, he enters a world teeming with microscopic organisms. This inaugural contact occurs suddenly at the moment of birth. The passage through the vaginal route, in the bacterial environment of the mother, marks the beginning of a cascade colonization which intensifies during the first hours. But in children born by cesarean section, the scenario changes. The pioneer bacteria then come mainly from the hospital environment, and not from the maternal intestine.
Researchers from University College London observed that on the fourth day of life, the intestinal microbiota begins to take a stable form. Before that, the newborn's stools still contain very little diversity. A study published in the journal Current Biology highlights that this implementation influences numerous physiological traits, such as metabolism, growth, behavior, but also immune regulation. Mice deprived of microbiota from birth, for example, have immature organs, a slowed metabolism and less protection against pathogens.
Over the weeks, the infant's microbial balance becomes more refined. Breastfeeding promotes a dominance of bifidobacteria, which are very present in human milk. This regime allows species like
Bifidobacterium breve to actively colonize the intestine and form a barrier against opportunistic microbes. On the other hand, antibiotics administered just after birth, even over a few days, can disrupt this balance. The study published in Nature in May 2025 reveals that this disruption profoundly modifies the microbial signature of affected infants, and affects their immunity for more than a year.
The infant's intestinal microbiota, the silent architect of health
These first bacteria are not harmless. Their role goes far beyond digestion. They train the immune system to recognize what is dangerous and what is not. The infant's intestinal microbiota acts as a guide, teaching the body to tolerate food antigens, control inflammatory responses and distinguish real threats from false alarms.
Work carried out at Bialystok hospital, reported in Nutrients, showed that the absence of bifidobacteria in infants born by cesarean section or exposed to early antibiotics increased their risk of developing food allergies or asthma. The link appears to come from an early alteration of immune tolerance. This initial dysbiosis (imbalance of the microbiota) leads to excessive activation of Th2 responses, involved in allergic reactions.
More recently, an Australian team demonstrated that this disruption also influenced the quality of the vaccine response. In infants who received antibiotics within days of birth, the amount of antibodies produced after injection of childhood vaccines such as pneumococcus or pertussis was significantly lower. This immune deficiency is accompanied by a depletion of bifidobacteria in the stools at the time of vaccination, confirming that certain key species of the microbiota contribute to immune memory.
In certain cases, the absence of a functional bacterial flora can even compromise the production of operational antibodies. The researchers demonstrated a reduction in opsonophagocytic activity (the ability of antibodies to signal microbes to be eliminated) in children whose microbiota had been altered from the first 48 hours of life.
Microbial engineering and targeted supplementation, promises and limits
Faced with these observations, the temptation to act early is great. Can we restore a beneficial microbiota in infants born by cesarean section or who have received antibiotics? Several avenues are explored, but none are unanimously accepted.
The most publicized is “vaginal seeding”, a process consisting of applying maternal vaginal secretions to the face and body of the newborn. The goal is to inoculate the child with the bacteria missed during delivery. However, this practice remains risky. The researchers behind the study relayed by the BBC point out that the microbes transmitted in this way are not the good ones. It is not the vaginal bacteria but those of the intestine that build a robust microbiota. In addition, this action could carry potentially dangerous pathogens.
More seriously studied, supplementation with oral probiotics, particularly based on Bifidobacterium breveseems more promising. These microorganisms, naturally present in breast milk, could restore certain impaired immune functions. Clinical trials have shown that they can reduce the risk of intestinal necrosis in very premature babies and even improve the response to certain vaccines. But again, each microbiota being unique, the effectiveness of these probiotics varies from one child to another.
At the same time, research is moving towards personalized solutions. The concept of precision microbial medicine is beginning to emerge. This would involve establishing an immune and microbial profile of the infant from birth to adapt care, food supplements, and even vaccination protocols. For the moment, this revolution remains experimental, but it could one day transform the way we think about baby health.
With an unwavering passion for local news, Christopher leads our editorial team with integrity and dedication. With over 20 years’ experience, he is the backbone of Wouldsayso, ensuring that we stay true to our mission to inform.
