Early prenatal antibiotic usage has limited impact on the microbiomes of infants

Abstract Background Antibiotic resistance poses an increasingly significant challenge to public health. The human gut microbiome is a reservoir for antibiotic resistance genes (ARGs), and ARG carriage is particularly high in infants compared with adults. Here, we investigate the gastrointestinal microbiome in a cohort of mothers and their born-to-term infants sampled during pregnancy and at 3- 6- and 12-months of age using deep shotgun metagenome sequencing of fecal DNA. Results Despite a high level of taxonomic individuality, the infant ARG complement showed strong temporal structure in terms of composition, with decreasing dispersion and increasing diversity up to the first birthday, while the lowest levels of dispersion and highest diversity were observed in the mothers. ARG abundance decreased over time to levels comparable with adults at 12 months. These trends were also observed for genes encoding known virulence factors. We also assembled plasmid sequences and found similar temporal structure, but without any significant change in abundances over time. Surprisingly, at no time point did the infants microbiomes resemble those of their own mothers more than those of unrelated women with respect to taxonomic composition, ARGs and VF gene content. We found minimal impact of pre-partum antibiotic use on the infant microbiome. Furthermore, antibiotic treatment during early infancy only had a minor impact on the microbiome at later time points. Conclusions This study adds to a growing body of literature demonstrating the temporal structure of key elements of the gut microbiome during infancy and offers some positive insights with respect to moderate exposure to antibiotics.