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expert reaction to study looking at birth method and mother-infant microbiota transmission and infant microbiota development

A study published in Cell Host & Microbe looks at birth method and infant microbiome development.


Prof Andrew Shennan, Professor of Obstetrics, Department of Women and Children’s Health, King’s College London, said:

“Women who give birth by caesarean may miss out on transmitting beneficial bacteria to their baby obtained in the birth canal.  This well-conducted study demonstrated that the baby may get this benefit through other routes, including breastfeeding.  They demonstrated that most of the babies’ bacteria (58%) actually comes from the mother regardless of the route of delivery.  Given the increasing caesarean section rate, women will find this reassuring.”


The following comments were provided by our colleagues at German SMC:

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.”

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.”

COI: “For my research project I receive funding from the German Federal Ministry of Education and Research.”


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, said:

“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.”

COI: “I have no potential conflicts of interest.”

[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.


The following comments were provided by our colleagues at SMC Spain:

Prof Dr Carmen Muñoz Almagro, Head of the Infectious Diseases and Microbiome research group and director of the Microbiology Laboratory, Sant Joan de Déu Hospital, Barcelona, Spain, said:

“This is a well-designed study, conducted by a research group with extensive experience in the study of the development of the human microbiome in the first months of life. The researchers demonstrate, using an appropriate methodology, how microbial transmission from mothers to their newborns is a multifactorial phenomenon, and they confirm the relevance of breastfeeding. They report that the differences in the microbiota of babies born by caesarean section and vaginal birth are not significant, since the lower microbial transfer by caesarean section is compensated by a higher transfer through breastfeeding.”

The author has declared they have no conflicts of interest.


Mireia Valles-Colomer, PhD, Researcher at the Computational Metagenomics Lab-CIBIO of the University of Trento, Italy, said:

“This study complements previous ones on the transmission of the microbiome from mother to baby. We know that, during childbirth, we acquire the first bacteria that will form our microbiome, which plays a very important role in our health. As a result, babies born by caesarean receive fewer bacteria from their mothers’ gut microbiome than those born vaginally.

“In this study, the authors analyse various types of samples from 120 mothers in the Netherlands (faeces, milk, skin, vaginal, saliva…) to study the contribution of these microbiomes in shaping the baby’s microbiome. In terms of the number of samples, the study extends, in which only babies born vaginally were included. The main conclusion of the study is that the lower transmission of the mother’s gut microbiome in babies born by caesarean section may be compensated for by the mother’s other microbiomes. But in terms of methods, the technique used is problematic: the authors only sequenced part of the 16S gene of the bacteria, instead of sequencing whole genomes, as other transmission studies have done to date. Thus, the resolution obtained is limited, and it is not possible to speak unequivocally of transmission.

“Regarding the press release, the title ‘Whether born naturally or via caesarean section, babies receive essential microbes from their mothers’ is something we already knew: babies born via caesarean section receive fewer intestinal microbes from their mothers, but they do receive some.”

The author has not responded to our request to declare conflicts of interest.



‘Mother-infant microbiota transmission and infant microbiota development across multiple body sites’ by Debby Bogaert was published in Cell Host & Microbe at 16:00 UK time on Wednesday 8 March 2023.

DOI: 10.1016/j.chom.2023.01.018

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