Baby-to-baby strain transmission shapes the developing gut microbiome.

Baby-to-baby microbiome transmission within nursery groups was detected even after only 1 month of nursery attendance.

• The study used a metagenomic survey to model microbiome transmission in the nursery setting.
• Dense longitudinal microbiome sampling was performed with n=1,013 faecal samples.
• The study included n=134 individuals comprising babies, their educators, and their families.
• Transmission was tracked within and between nursery groups across 3 different facilities.

Nursery-acquired strains accounted for a proportion of the infant gut microbiome comparable to that from family by the end of the first nursery term.

• The study tracked microbial strain transmission longitudinally during the first year of nursery.
• The contribution of nursery-acquired strains grew to be comparable in magnitude to family-derived strain contributions.
• This finding highlights that non-familial social settings become major microbiome contributors early in life.

Baby-to-baby transmission continued to grow over the nursery year, forming an increasingly intricate transmission network.

• Single strains were observed spreading across entire classes in some instances.
• The transmission network became more complex over time with multiple baby-acquisition patterns.
• Species-transmissibility patterns were identified, indicating that some microbial species were more readily transmitted than others.

Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers.

• The presence of siblings in a household was identified as a variable associated with microbiome diversity outcomes.
• Infants with siblings acquired fewer strains from nursery peers compared to infants without siblings.
• This suggests that prior exposure to non-parental transmission sources modulates subsequent nursery-based acquisition.

Antibiotic treatment was the condition that most accounted for increased influx of strains from nursery peers.

• Among conditions examined, antibiotic treatment showed the strongest association with increased strain acquisition from nursery.
• This finding suggests that antibiotic-induced microbiome perturbation increases susceptibility to colonization by external strains.
• The result points to antibiotic use in infancy as a key modulator of microbiome transmission dynamics.

The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life, but interpersonal transmission in nursery settings further shapes microbiome development in the first year.

• Prior literature established maternal transmission as the primary early microbiome source.
• This study extends the understanding of microbiome development by characterizing non-maternal, peer-based transmission.
• The nursery setting was used as a model for studying interpersonal microbiome transmission beyond the family unit.