Antibiotic resistance in human pathogenic bacteria has increased dramatically over the past decades, challenging our ability to treat bacterial infections. Pathogens can acquire resistance to available antibiotics within months, often through genetic exchange with diverse microbial reservoirs. Such reservoirs include the human microbiota (microbiome), the vast collection of bacteria that live within the human body. New molecular methods using next-generation DNA sequencing demonstrate that many reservoirs of antibiotic resistance genes (or "resistomes") have been profoundly under-sampled using traditional culture-based methods. Dr Dantas recently used approaches based on next-generation DNA sequencing to discover and characterize a large number of novel resistance genes from the microbiota of adults. This proposal aims to further develop these methods to investigate the diversity and development of antibiotic resistance genes in the microbiota of children, from birth through their first few years of life. Bacterial communities quickly colonize the sterile guts of newborns, with gut communities exhibiting a remarkable variability over the first two years of life, after which the dramatic swings in bacterial populations subside. Hence, the mechanisms that underlie the development of the resistome in an individual’s microbiota are most effectively studied in the post-natal period. Samples from both healthy and sick children will be analyzed, to investigate the role of factors such as genetics and antibiotic treatment in the development of antibiotic resistance genes in the developing microbiota. These studies will leverage ongoing work of other Children's Discovery Institute researchers in the St Louis Gut Neonatal Microbiome Initiative (Drs. Warner, Gordon, Tarr and Hamvas). Results from this proposal should provide novel translational data and enable further studies to curb the transfer of antibiotic resistance genes to pathogens.