Gut microbiota development, antibiotic resistome, and related perinatal factors in early infancy

Early life is a critical window for gut microbiota development and antibiotic resistome. We aimed to investigate the microbiota longitudinal change during the first 6 months of life and the differences associated with assisted reproductive technology (ART) treatment, mode of delivery, and infant sex. Gut microbiota was measured by metagenomic sequencing of fecal samples repeatedly collected within 3 days after birth, at 42 days, 3 months, and 6 months in 155 Chinese infants. Among infants born by vaginal delivery, the ACE, Chao, and Sobs indexes increased with age. Accordingly, the relative abundance of Actinobacteria phylum increased from 43% ± 37% (mean ± SD) to 57% ± 36% and Proteobacteria phylum decreased from 48% ± 36% to 17% ± 25%; and Bifidobacterium and Klebsiella genus increased and Escherichia genus decreased, from the first 3 days to 6 months. The dominant antibiotic resistance genes were macB and msbA. Boys and girls had similar features. Infants born by cesarean section exhibited a similar gut microbiota developmental trajectory, but with a slower increase in alpha diversity over time, and lower Bacteroidetes phylum and Bacteroides genus at each age point. Compared with non-ART infants, ART infants had slightly higher alpha diversity indexes of ACE, Chao, Sobs, Shannon, and Pielou's evenness at age 42 days among infants born by vaginal delivery. Our findings confirm increasing diversity and composition evolution of gut microbiota in the first 6 months of life. Both modes of delivery and ART conception are associated with early gut microbiota alteration.IMPORTANCEGut microbiota plays an important role in various aspects of human health. Early life is a critical period for the development of gut microbiota. In this prospective study, we observed that the diversity and antibiotic resistance genes of gut microbiota increased gradually with age in the first 6 months of life. Boys and girls had similar features of gut microbiota. Cesarean section was associated with a lower abundance of Bacteroidetes phylum and Bacteroides genus. Compared with non-ART infants (spontaneous conception), ART infants had slightly higher alpha diversity indexes of ACE, Chao, Sobs, Shannon, and Pielou's evenness at age 42 days among infants born by vaginal delivery. This study presents gut microbiota development with age, antibiotic resistome, and related perinatal factors in early infancy.