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Birth Defects Res C Embryo Today. 2015 Dec;105(4):240-51. doi: 10.1002/bdrc.21113. Epub 2015 Nov 26.

On the origin of species: Factors shaping the establishment of infant's gut microbiota.

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Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany.
Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands.
Department of Medical Microbiology and Infection Control, VU University Medical Center Amsterdam, The Netherlands.
Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Centre+, Maastricht, The Netherlands.


The human gut microbiota is a complex and dynamic ecosystem, which naturally lives in a symbiotic relationship with the host. Perturbations of the microbial composition (dysbiosis) and reduced diversity may promote disease susceptibility and recurrence. In contrast to the mature intestinal microbiota of healthy adults, which appears relatively stable over time, the infant's microbiome only establishes and matures during the first years of life. In this respect, early childhood seems to represent a crucial age-window in disease prevention, since microbial diversification and maturation of the microbiome primarily occurs during this period of life. A better understanding of ecological processes and pioneer consortia in microbial development is crucial, in order to support the development of a beneficial microbiota. Various deterministic and stochastic aspects seem to shape the microbiome in early life, including maternal, environmental, and host factors. Here, we review the current understanding of the origin of pioneer bacteria and the evolutionary factors that influence the development of the gut microbiota in infants. In addition, future perspectives, including manipulating and promoting the succession of initial bacteria during infancy, will be highlighted.


antibiotics; cesarean section; diet; ecology; microbiome

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