Temporal dynamics and functional maturation of the infant gut microbiota during the first year of life

BACKGROUND: The infant gut microbiota undergoes structured, time-dependent succession during the first year of life, yet high-resolution longitudinal characterization remains limited. Here, full-length 16S rRNA gene sequencing was performed using PacBio long-read technology on 68 fecal samples from 12 exclusively breastfed infants in Hohhot, China, across six time points from birth to one year (7, 30, 60, 100, 200, and 360 days). RESULTS: In this study, 68 fecal samples from 12 infants were analyzed. A total of 16 bacterial phyla, 192 genera and 251 species were annotated, with the dominant phyla being Firmicutes, Actinobacteriota and Proteobacteria; the dominant genera including Bifidobacterium, Streptococcus and Escherichia-Shigella; and the dominant species comprising Streptococcus_salivarius, Bifidobacterium_longum and Bifidobacterium_pseudocatenulatum. Alpha diversity generally increased by days 360, while community composition shifted from early Bifidobacterium dominance toward greater taxonomic and functional complexity. Permutational multivariate analysis of variance (PERMANOVA) revealed that host and environmental factors collectively explained 33.92% of community variation (P = 0.001). Six temporal colonization patterns were observed through MaAsLin2 analyses., including mid-term explosive and sustained increasing trajectories. Functional profiling using Tax4Fun2 revealed time-specific enrichment of metabolic pathways, including fatty acid biosynthesis, xenobiotic degradation, and autophagy regulation at day 360. The findings of this longitudinal study be interpreted considering its modest sample size (n = 68). Future studies with larger cohorts are needed to validate and generalize these observations. CONCLUSIONS: These findings demonstrate that infant gut microbiota assembly follows a non-random, host-guided trajectory, with dietary transitions and microbial interactions driving structural and functional maturation, providing a high-resolution framework for understanding early-life microbiome development and its implications for infant health. However, due to the limited sample size, the relevant research results have certain limitations. In the future, it is necessary to expand the sample scale and conduct more convincing studies.