The pilot study was conducted on samples from mother–infant pairs from the CELSPAC:TNG cohort. It offers a comprehensive look into how the diet shift transforms child's oral and gut bacteriomes and fecal metabolome.
The prospective, longitudinal study showed that infants’ oral and gut microbiota change substantially during the first year of life, particularly as solid foods are introduced. In the mouth, bacterial diversity increased, with Streptococcus and Gemella, common early colonizers, becoming less dominant, while bacteria such as Neisseria, Porphyromonas and Granulicatella became more abundant.
In the gut, the initially dominant Bifidobacterium, a group of bacteria well adapted to life on human milk, gradually gave way to bacteria such as Blautia and Intestinibacter, contributing to a richer and more complex gut community. Greater microbial diversity is generally considered an important feature of a healthy, well-functioning gut.
"These changes were accompanied by changes in the substances produced or modified by gut microbes. As the infants grew and their diets became more varied, short-chain fatty acids (SCFAs), including acetate and propionate, steadily increased. SCFAs are important products of bacterial fermentation of food that can provide energy for the body, support intestinal health and contribute to the proper functioning of the immune system," explains Jan Böhm, one of the co-authors and a PhD student of Environmental Health Sciences program.
The study was conducted in cooperation with the University of Cagliary. Scientists at RECTOX analyzed oral and fecal bacteriomes of breastfed children using 16S rRNA amplicon sequencing. And the scientific team at the University of Cagliari analyzed metabolomes of these fecal samples as well as human milk samples using Nuclear Magnetic Resonance (NMR).
The study was recently published in Pediatric Research journal (Q1) – an official journal of the American Pediatric Society and the European Society for Pediatric Research. The first co-author of this publication, together with Jan Böhm, is Eliška Pivrncová who also received her PhD from the Environmental Health Sciences at RECETOX.
This research was supported by the EDUC project and the Horizon Europe ENDOMIX project. DOI: 10.1038/s41390-026-05354-0
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