Previous studies at the Cibio Department observed microbe transmission from mother to infant at birth and among cohabiting adults. The dynamics of how the early life microbiome assembles into a complex and individual ecosystem in adulthood remained poorly understood. This study aimed to address this gap.
Study Hypothesis and Methodology
Researchers hypothesized that the first social contexts, such as daycare centers, could be sites for gut microbe exchange and acquisition, shaping the microbiome during the initial thousand days of life. The analysis focused on how bacterial components of the microbiome are acquired.
The study included 134 individuals: 41 babies aged 4 to 15 months attending their first year of daycare (from six classes across three facilities), their parents, siblings, family pets, and daycare educators and staff. Samples were collected regularly for an entire school year (September 2022 to July 2023). These samples were then analyzed using metagenomic sequencing and bioinformatic techniques. This enabled the profiling of individual variants of bacterial species (strains) and mapping their sharing and transmission among individuals over time, utilizing new computational methods developed by the research group.
Key Findings: The "Social" Microbiome
Liviana Ricci, a research fellow at the Cibio Department and first author, stated that during the first three months, the number of shared strains began to increase among members of the same class but not across different nurseries. Initially, babies typically had no strains in common. By the study's conclusion, babies, on average, shared approximately 20 percent of strains with at least one other baby in the same nursery.
Vitor Heidrich, co-first author, described tracking a single strain of Akkermansia muciniphila, a common gut bacterial species. Its transmission was traced from a mother and baby to a peer in the same class, and subsequently to the peer's parents, where it even replaced an existing resident strain. Similar transmission patterns were identified for many distinct strains across hundreds of different bacterial species, creating an intricate map of microbial transmission.
Nicola Segata, Professor of Genetics at the Cibio Department and study coordinator, highlighted that sharing spaces and social interaction with peers in the first year of life contributes to microbiome development as much as acquiring it from family members. This process helps define the unique set of bacteria each individual carries.
Impact of Antibiotics and Future Implications
Another aspect of the study concerned the impact of antibiotic treatments on microbiological transmission dynamics. Segata noted that antibiotics not only eliminate pathogens but also decrease the quantity and bacterial diversity of the microbiome as a side effect. However, in infants, an increase in the acquisition of new strains or species from peers was observed in the period following antibiotic treatment. This suggests that the intestinal imbalance induced by antibiotics might make the infant gut microbiome more receptive to acquiring external bacteria, thus aiding in restoring a more adequate microbial configuration.
This fundamental knowledge could lead to future microbiome-based intervention strategies. Segata mentioned that artificial microbiome transmission, such as fecal transplants in certain categories of cancer patients undergoing immunotherapy, has been successfully attempted in other studies. Understanding transmission patterns could inform prevention strategies and targeted biotherapeutic approaches. The success of the study was attributed to multidisciplinary teamwork and collaboration among all daycare staff, Trento municipal offices for childhood services, and the involved families.
The article "Baby-to-baby strain transmission shapes the developing gut microbiome" is part of the ERC project "MicroTouch" and was published in Nature.