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Microbiome transfer from mother to child


  • according to a study, babies receive essential microorganisms from the mother in the first weeks of life, irrespective of the birth method

  • after a caesarean birth, microorganisms can be transferred mainly through breastfeeding  

  • researchers welcome the findings that babies have a no deficit of maternal microbes after a caesarean birth 

The colonization of a newborn child with microbes from its mother takes place via several pathways, such as skin contact, breast milk or vaginal secretions, which together provide the baby with an arsenal of microbes. These transmission pathways act redundantly and compensatory, for example, if the transfer of microbes from the vaginal secretion fails to occur during a caesarean birth. This finding is presented by a Dutch research team from Utrecht in the scientific journal "Cell Host & Microbe" (see primary source).

In their work, they investigated the extent to which microbes from different niches – sources such as the nose, skin, breast milk and others that have a characteristic composition of microbes – contribute to the colonization of the baby. For this purpose, they analyzed samples from 120 mother-child pairs. They took samples from the mothers' nasopharynx, saliva, breast milk, skin, vaginal secretions and stool – shortly before and up to one month after birth. Swabs were taken from the nasopharynx, saliva, skin and stool samples of the newborns. Using the sequencing data, they were able to track which microbe species were transmitted directly from mother to child.

On average, 58.5 percent of the microbial composition of infants came from the mother – regardless of the delivery method. However, the researchers found differences in which source the babies received the proportions of maternal microbes from. Whereas babies delivered vaginally already receive microbes from the birth channel, children after a caesarean birth receive more microbes through their mother's milk. The authors point out that breastfeeding after a caesarean birth is therefore particularly important.

Based on previous studies, it was assumed that children born by caesarean section have a deficit of maternal microbes because they do not come into contact with the microorganisms from the birth channel and the gut. To compensate for this loss, the method of 'vaginal seeding' has been studied and discussed in recent years [1]. This involves wiping a cloth over the baby's mouth and nose after birth, which has previously been covered with vaginal fluid. This is supposed to give the child the necessary microorganisms afterwards.

The SMC asked researchers to what extent the evaluation of the Dutch researchers shows that this deficit can really be compensated for via alternative natural transmission routes and thus makes subsequent transmission via vaginal seeding dispensable.



  • Prof. Dr. Bernhard Resch, Deputy Head of the Clinical Department of Neonatology and Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Austria

  • Prof. Dr. Christoph Härtel, Director of the Paediatric Clinic and Polyclinic, Würzburg University Hospital


Prof. Dr. Bernhard Resch

Deputy Head of the Clinical Department of Neonatology and Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Austria

„The study is well planned and very well powered with 120 mother-infant pairs.“

„It is very plausible to me that the microbial transfer between mother and child takes place via multiple routes.“

„This puts the caesarean birth, which is particularly necessary when the child is in acute danger, back into perspective. Giving more reason to support and promote breastfeeding after caesarean section.“

When asked if it is plausible that other routes of microbiome transfer can compensate for vaginal microbiome transfer in the baby:
„Now that the entero-mammarian pathway seems pretty much proven – the pathway of microbes from the maternal gut to the mammary glands – it makes perfect sense: ‘From Mother’ s Gut to Milk.' It would also certainly not be intended by nature to include only one colonisation pathway. And it seems much more attractive to me to put the baby to your bosom after a caesarean than to wipe his face with a vaginal secretion-soaked cloth.“

When asked if it can be deduced from the data that the method of vaginal seeding is redundant and can be absorbed by breastfeeding:
„That’s how it seems to me! From the point of view of the number of germs, it will take longer than after ‘vaginal seeding’ for the same amounts of microbes to reach the child. In the context of the rapid changes over the first two weeks until a balanced, abundant and good infant microbiome is achieved, it is probably not necessary to have such high microbial densities as are possible after vaginal seeding. What was fascinating about Dominguez-Bello’s work, however, was that this method of ‘vaginal seeding’ leaves a microbiome in the newborn that corresponds to the vaginal microbiome and is also permanent [1].“

When asked to what extent the authors’ statement is plausible that, evolutionarily, it makes sense for transmission routes to be redundant:
„That statement is right up my alley. It’s always fascinating to see what evolution has come up with that we are slowly beginning to explore and understand after millennia.“

Prof. Dr. Christoph Härtel

Director of the Paediatric Clinic and Polyclinic, Würzburg University Hospital, Germany

„This is a sound and very comprehensive study in which the researchers investigated the pathways of microbial transmission from mother to child after birth. The authors of the study very carefully examined various skin and mucosal niches in 120 mother-child pairs over the first weeks of life. In doing so, they consistently checked at which niches of the child the mother’s microbes accumulate and from which resource niche they originate.“

„We know that C-section babies have certain risks for asthma and obesity. One reason for this could be a different microbiome than in children born vaginally. A second possible reason may be antibiotics given to the mother during the caesarean section. It was under this assumption that all the ‘vaginal seeding’ ideas came about. C-section babies lack the microbiome from the birth canal. We know that in the last four weeks before birth, the mother’s microbiome changes in the birth canal to give the baby a boost of ‘good’ bacteria at birth. If that’s missing, then the child first colonises differently, probably mainly through the skin. Vaginal seeding, the inoculation with vaginal bacteria after birth by swabs, is a potential means to compensate for that.“

„Mothers of C-section babies – and their parents in general – often wonder if there is anything they can do for the child to help with its microbiome. The study provides a first positive message, which we actually always give to the women after birth: lots of cuddling, lots of breastfeeding. This compensates for the lack of exposure with vaginal flora. And that’s what this study now shows as well.“

When asked if one can deduce from the data that the method of ‘vaginal seeding’ is redundant and can be replaced by breastfeeding:
„It has not yet been proven in studies that ‘vaginal seeding’ has a long-term positive effect on, for example, the risk of asthma or obesity. Seeding has shown positive effects in the context of studies, but it also carries possible risks, such as the transmission of viruses, which is why this method has not yet been recommended by professional societies. Now we have the first proof that you don’t necessarily have to do it – that’s very relieving.“

„The data show that caesarean babies benefit very much from breastfeeding, and much more quickly than babies delivered vaginally. And the amount of cuddling – as in contact with the mother’s skin so that the microbiome is transferred to the child – provides a higher diversity of microbes, which again is protective. It would be interesting to study whether the children who received a lot of cuddling and breastfeeding then go on to develop for example less asthma.“

When asked if breastfeeding can compensate quantitatively (microbiota quantity) or qualitatively (microbiota composition) for microbiota transmission:
„We see differences in the pioneer bacteria, that is, the first species of bacteria that colonise the child, because the first transmission is different. However, one cannot look at the microbiome in isolation, but must always think of it as part of a complex system, because it also interacts with the immune and metabolic system, among other things. The microbes produce metabolic products, which in turn contribute to the maturation of organs. Microbes colonise our whole body and contribute to our health. There is a specific microbiome in the lungs and in the gut: how do the bacteria communicate with each other, how do the microbes in the gut communicate with the brain? The bottom line is that you can’t say that you can probably solve all problems just by breastfeeding. Breastfeeding can have an almost one-to-one beneficial effect on gut colonisation, and it lowers the risk of asthma, but we have not yet proven that this is due to the pioneer bacteria being different in asthma patients compared to healthy individuals. This requires long-term, complex studies that also include effects on other components, such as the immune system or metabolism. But the authors also commented on these limitations very defensively.“

When asked to what extent the authors’ statement is plausible that it makes evolutionary sense for transmission pathways to be redundant:
„Nature has designed the maturation and development of children to equip the child in a healthy way. Nature is able to adapt when a pathway cannot be taken. Another example: some newborns suffer a stroke, but nature’s plasticity can manage at this early stage of development to sprout alternative auxiliary pathways that help to take over the function of the stroke area by other brain regions. This does not exist in adults. So, it seems logical that there are different pathways and adaptations for the child to get to the microbiome it needs, even if there are risk factors, such as the mother not being able to breastfeed or being given antibiotics.“

Conflict of interest

Prof. Dr. Bernhard Resch: „I have no potential conflicts of interest.“

Prof. Dr. Christoph Härtel: „For my research project I receive funding from the German Federal Ministry of Education and Research.“

Primary reference

Bogaert D et al. (2023): Mother-infant microbiota transmission and infant microbiota development across multiple body sites. Cell Host & Microbe. DOI: 10.1016/j.chom.2023.01.018.

Further research sources

Science Media Center (2019): Gestörte Erstbesiedelung des Darmmikrobioms nach Kaiserschnitt. Research in Context. 18.09.2019.

Science Media Center (2022): Einfluss der Geburtsmethode auf Mikrobiom und Impfantwort. Research in Context. 15.11.2022.

References, cited by experts

[1] Dominguez-Bello M et al. (2016): Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine. DOI: 10.1038/nm.4039.

[2] Ferretti P et al. (2018): Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host & Microbe. DOI: 10.1016/j.chom.2018.06.005.