OOS 26-4
Microbiome dynamics in healthy children from birth to age two: Playing out the consequences of disturbance and dispersal limitation in developing gut, oral, and skin communities
The first two years constitute a critical period in human development. Microbial exposures, timed specifically to this period, likely modulate long-term metabolic and immune functioning in the host. Yet our knowledge of the assembly of the infant-associated microbiota – of the detailed patterns, prevailing processes, and developmental milestones – is incomplete. Here, we characterize the gut, oral, and skin microbiota of 15 healthy infants sampled longitudinally from birth to age two, using sparse (thrice monthly) time series at baseline and dense (daily) time series around courses of antibiotics, if and when they occurred. We also characterize the postpartum gut, oral, skin, vaginal, and breast milk microbiota of the mothers at 6-month intervals. Bacterial 16S rRNA gene surveys were carried out for all samples, while shotgun sequencing, followed by time series community genomics analysis, was carried out for a subset.
Results/Conclusions
The rate and pattern of microbiome assembly depended on body site; gut communities exhibited a strong developmental program, while skin communities reflected environmental exposures paralleled in the mother. The level of interpersonal variation also depended on body site, but also on age. Initial dispersal limitation, in the form of delivery via Cesarean section (n = 5 infants), left a strong mark on gut communities, where the expansion of Bacteroides spp. (important denizens of this body site) was profoundly delayed. Seven of the infants received one or more courses of antibiotics, with oral amoxicillin for ear infection most common. Antibiotics impacted communities at all body sites, but to varying degrees. In the gut, and as viewed through the lens of 16S rRNA gene surveys, communities were largely (and quickly) resilient. However, time series community genomics analysis (of samples collected before, during, and after antibiotics) reveals additional dynamics, likely mediated by phage, plasmids, and other mobile elements.