Babies acquired a greater proportion of gut microbial strains from nursery peers than from family members after 3 months of nursery attendance, according to a recent study.

Researchers found that baby-to-baby microbial transmission in nursery settings was associated with changes in infant gut microbiome composition during early attendance. In a longitudinal, strain-resolved metagenomic analysis, microbial strain sharing among infants increased over time, reaching more than 20% by the end of the first nursery term and continuing to rise across the nursery year.

The microTOUCH-baby study evaluated interpersonal microbiome transmission in early childhood beyond the household environment. The cohort included 134 participants recruited from 3 public nurseries in Trento, Italy, including 43 babies, their parents, siblings, educators, and household pets. Infants were enrolled at a median age of 10 months. Stool samples were collected weekly from babies during the first nursery term, with additional sampling through the end of the nursery year and after the summer break. Overall, 1,013 fecal samples were analyzed using shotgun metagenomic sequencing at an average depth of 15.6 Gbp.

Species-level genome bin profiling was conducted using MetaPhlAn 4, and strain-level transmission was inferred with StrainPhlAn 4. Before nursery attendance, infant gut microbiomes showed expected patterns, including strong maternal contributions, with a median mother–baby strain-sharing rate of approximately 50%. Within 1 month of nursery exposure, however, strain sharing among infants attending the same nursery group increased significantly compared with infants from different nurseries.

By the end of the first nursery term, the average number of strains shared between babies increased from 2.5 at baseline to 7.2, and strain-sharing rates within the same nursery group reached a mean of 20%. The proportion of strains acquired from nursery peers increased from 6.5% at baseline to 28% at 3 months, surpassing the proportion attributed to family transmission.

“After only 3 months of nursery attendance, babies had proportionally more strains acquired from nursery peers than from their family,” wrote lead researcher Liviana Ricci, PhD, of the University of Trento in Italy, and colleagues.

In terms of relative abundance, nursery-derived strains accounted for nearly 40% of the infant gut microbiome by the end of the first term. Infants also exhibited marked microbiome plasticity, with 44% of retained species-level genome bins undergoing strain replacement over 5 months, compared with less than 11% among adults. Antibiotic exposure was associated with reduced strain retention and increased acquisition of new strains, particularly in infants, whereas having siblings was associated with higher baseline microbiome diversity and reduced acquisition of strains from nursery peers.

Several limitations were noted. The cohort was geographically limited to a single Italian city, which may affect generalizability. Strain-level analyses focused on dominant strains, potentially underestimating transmission of low-abundance strains. Parents and educators were sampled less frequently than infants, which may have limited detection of adult-to-infant strain sharing. The observational design also precluded causal inference.

The researchers reported no competing interests.

Source: Nature