Previous studies conducted in the same laboratory of the Cibio Department had observed the transmission of microbes from the mother to the infant starting from birth, and then the transmission among cohabiting adults. But the dynamics of how the early life microbiome is assembled in the few years after birth to become a complex and individual ecosystem in adulthood is still poorly understood. This article could help bridge the gap.
About the study. The initial hypothesis of researchers was that the first social contexts in a human being's life, such as daycare centres, could be places where gut microbes are exchanged and acquired. This process shapes the microbiome during the first crucial thousand days of an individual's life. The analysis therefore focused on how the bacterial components of the microbiome are acquired, and the researchers found the answer: they are acquired not only from family, but also - and perhaps more so - from society. The study involved 134 individuals. Of these, 41 are babies between 4 and 15 months of age (six classes from the three facilities) attending their first year of daycare, their parents, siblings, and family pets, as well as educators and staff working at the daycare centres. For an entire school year, from September 2022 to July 2023, samples were regularly collected for each participant. These were then studied through metagenomic sequencing and bioinformatic techniques. This made it possible to profile individual variants of bacterial species (strains) and map their sharing and transmission among people over time, thanks also to new computational methods specifically developed by the research group.
The "social" microbiome. "We observed," explains Liviana Ricci, research fellow at the Cibio Department and first author of the article, "that during the first three months, the number of strains began to be shared by members of the same class, but not by those attending different nurseries. Initially, therefore, the babies typically had no strains in common with each other. At the end of our study, we found that, on average, babies shared about 20 percent of the strains with at least one other baby in the same nursery." In one of the results described in the study, for example, the authors tracked a single strain of Akkermansia muciniphila (a common gut bacterial species). "We traced its transmission," explains Vitor Heidrich, also a research fellow at the Cibio Department and co-first author of the study who handled the computational data analysis, "from a mother and baby of the same family to a peer in the same class and finally to their parents, where it even replaced an existing resident strain." Similar tracking was identified for many distinct strains of each of the hundreds of different bacterial species, generating an extremely intricate map of microbial transmission.
This is a significant result for the researchers. "Sharing the same spaces and social interaction in the first year of life with peers contribute to the development of our microbiome as much as acquiring the microbiome from the members of one's own family, and this leads to defining the unique set of bacteria that each of us carries," emphasizes Nicola Segata, Professor of Genetics at the Cibio Department and coordinator of the work. Another interesting aspect concerned the impact of antibiotic treatments on the dynamics of microbiological transmission. "Antibiotics not only eliminate the pathogen for which it is prescribed but also decrease the quantity and bacterial diversity of the microbiome as a side effect. In infants, however - and this is the novelty," Segata points out, "we noticed an increase in the acquisition of new strains or new species from their peers in the period following antibiotic treatment. This is probably because the intestinal imbalance induced by the antibiotic made the infant gut microbiome more prone to acquire external bacteria and thus restore a more adequate microbial configuration."
The practical implication of this basic knowledge could lead to future microbiome-based intervention strategies. "The use of artificial microbiome transmission through fecal transplants in certain categories of cancer patients in immunotherapy, for example," Segata anticipates, "has already been successfully attempted in other studies to which we contributed. Understanding transmission patterns could lead to prevention strategies and targeted biotherapeutic approaches." Collaboration among all daycare staff, Trento municipal offices for childhood services, and the families involved was essential for the success of the study. "This was truly multidisciplinary teamwork," the research group emphasizes, "and proves that science can make a significant impact when built together with the community."
About the article
"Baby-to-baby strain transmission shapes the developing gut microbiome" is part of the Erc project "MicroTouch", coordinated by Nicola Segata. It is available in Nature: https://www.nature.com/articles/s41586-025-09983-z
Doi: https://doi.org/10.1038/s41586-025-09983-z
