Temporal dynamic development and assembly of gut microbiota in healthy infants during the first year of life

The process of microbial development plays a vital role in infant health, but the developmental characteristics of the infant microbiota remain elusive, especially in the first year of life. Here, we recruited 36 healthy Chinese mother–infant pairs and longitudinally collected 630 fecal samples for 16S rRNA gene high-throughput sequencing and whole metagenomics sequencing, respectively, including infants fecal samples collected at 27 time points from birth to one year, and maternal fecal samples collected once after delivery. We demonstrated the landscape of temporal development of the gut microbiome. The infant microbiome clustered into three enterotypes and displayed dynamic transition, which was greatly impacted by dietary structure and delivery mode. Notably, the microbial community assembly analysis revealed that the whole process of neonatal microbiota development was a mixture of deterministic (heterogeneous and homogeneous selection) and stochastic (neutral) processes, which comprised four stages with distinct ecological processes and microbial trajectory clusters. These findings highlight the temporal dynamic characteristics and process of gut microbiome assembly during the first year of life in infants.