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The Maturation of the
Infant Microbiota

The moment we enter the world, microbes colonize our bodies. And depending on how and where we're born, we're colonized by different types of microbes. However, a recent study of maternal-infant pairs suggests that the effect of caesarean birth on the microbiota assembly is rather small or non-existing.

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The maturation of the infant microbiota

In adults, body sites such as the skin, oral cavity, gut and vagina are characterized by distinct microbial communities. For example, Streptococcus species generally dominate the oral cavity, whereas Lactobacillus species are generally characteristic for the vagina (1). It is not completely understood how the microbiota assembles and when body site differentiation is achieved. Furthermore, how this assembly process may be altered by exogenous factors, such as mode of delivery and breastfeeding practises, is not fully understood. Nonetheless, several studies have shown that babies born by caesarean delivery harbour a different microbiota than babies born by vaginal delivery. However, a recent study of maternal-infant pairs suggests that the effect of caesarean birth on the microbiota assembly is rather small or non-existing (2). 



The infant microbiota _803


     Illustration by Nishant Choksi


This study assessed the microbiota 6 weeks after delivery across the skin, oral cavity, nostrils and gut, in both mother and child. Unlike the maternal microbiota, whose microbiota composition was primarily driven by the body sites, the neonatal microbiota did not demonstrate strong body site differentiation. 


By 6 weeks of age, however, the infant microbiota seemed to be primarily driven by body site differences, similarly to that of the maternal microbiota. The effect of caesarean mode of delivery on the composition of the microbiota was also determined. It was found that although patterns of microbial composition in neonates were influenced by mode of delivery at birth, these differences were absent in the infants at 6 weeks of age. This study shows that the infant microbiota undergoes substantial reorganization within the first 6 weeks of lifewhich is primarily driven by body site and not by mode of delivery. This selection may however be influenced by other factors, such as use of antibiotics and breastfeeding practises. 

Further research should determine the exogenous factors that may alter the assembly process. This could then result in early-on interferences that will ensure the assemble of a well-functioning microbiota. 


Our bodies have many habitats, each with their own characteristics. Each habitat is home to a different population of microbes
Read the scientific article 



(1)   Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial Community Variation in Human Body Habitats Across Space and Time. Science. 2009;326(5960):1694-7.

(2)   Chu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017). Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nature Medicine23(3), 314-326




The infant microbiota

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