Despite widespread use of antibiotics in children, the effects of antibiotic exposure on the developing infant gut microbiome have remained underexplored. Here, Yassour et al. present a longitudinal study capturing how the gut microbiome responds to and recovers from antibiotic perturbations. Antibiotic-treated children had less stable and less diverse bacterial communities. Antibiotic resistance genes within the guts of these children peaked after antibiotic treatment but generally returned rapidly to baseline. Delivery mode (vaginal versus cesarean) also had strong long-term effects on microbial diversity. These data give insights into the consequences of early life factors such as birth mode and antibiotic treatment on the infant gut microbiome.

The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life. Longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed detection of strain-level variation as well as the abundance of antibiotic resistance genes. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. Our results highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the infant gut microbiome.

We therefore undertook a natural history study of the infant gut microbiome with unique strengths arising from the combination of dense sampling, multiple clinical variables (including birth mode and antibiotic usage), and strain-level analysis. We collected and analyzed samples from 39 children with an average of 28 samples per child for the first 3 years of life. During this time period, 20 of the children received 9 to 15 antibiotic treatments, whereas the remaining 19 children never received antibiotics. We performed both 16S ribosomal RNA (rRNA) gene and whole-genome shotgun (WGS) sequencing to analyze microbial diversity at all taxonomic levels, including genus, species, and strain. In addition to gaining insight on how the gut microbiome develops when unperturbed by antibiotics, metagenomic sequencing of samples before and after antibiotic exposure allowed us to explore changes in the abundance of antibiotic resistance genes. We found decreased microbial diversity and increased short-term composition changes in the gut microbiomes of antibiotic-treated children. Furthermore, we observed an increased abundance of antibiotic resistance genes after treatment, along with concurrent increases in specific bacteria likely harboring these genes.

Fewer studies have sought to characterize the natural history of the gut microbiome in children. Most of these studies have attempted to infer the natural history based on cross-sectional data sets comparing multiple children at a single time point. These cross-sectional observations have reported that birth mode (vaginal delivery versus cesarean section) affects gut microbiome composition in the first 6 months of life ( 29 – 31 ) and that the gut microbiome of children matures by the age of 3 years ( 32 ). More recently, a longitudinal study analyzing four time points during the first year of life reported that birth mode and nutrition influence gut microbiome composition at the level of bacterial species ( 33 ). However, no longitudinal studies have analyzed the developing gut microbiome with dense sampling or detailed analysis at the level of strains within species. In addition, despite widespread use of antibiotics in children, the effect of antibiotic exposure on the developing infant gut microbiome remains unexplored. The high prevalence of antibiotic use and the concurrent increase in antibiotic-resistant bacteria, coupled with our growing appreciation of the microbiota's role in human health, highlight a critical need to understand the short- and long-term effects of repeated antibiotic treatments on the gut microbiome.

A growing number of studies have highlighted the critical role played by commensal bacteria in human health. These studies have largely focused on characterizing healthy adults ( 1 ) and finding commonalities among patients suffering from diseases such as inflammatory bowel disease ( 2 , 3 ), type 2 diabetes ( 4 ), obesity ( 5 – 9 ), metabolic disorders ( 10 – 15 ), colorectal cancer ( 16 , 17 ), liver cirrhosis ( 18 , 19 ), rheumatoid arthritis ( 20 ), and others. Several longitudinal studies have focused on pediatric conditions, including malnutrition ( 21 , 22 ), type 1 diabetes ( 23 ), and asthma ( 24 ). More recently,