Effects of peri-natal antibiotic administration in piglets on gut microbiota composition and antibiotic resistance gene prevalence Raw sequence reads

The swine gastrointestinal microbiota is comprised of a diverse and complex microbial population that coexists in a coordinated, complex mucosal ecosystem that contributes to host gastrointestinal and immunological development. It is important to understand how common management practices, such as antimicrobial administration, might affect this complex ecosystem and ultimately animal health. In addition, the emergence of antibiotic-resistant bacteria is an urgent public health issue creating pressure to reduce the use of antimicrobials. While the antibiotic resistance profiles of pathogens and opportunistic bacteria cultured from swine have been characterized, the Antimicrobial Resistance Genes (ARG) from the whole gut microbiota have received far less attention. Optimizing the use of antimicrobials in health management programs will require understanding antimicrobial-induced changes to both the gut microbiota and the prevalence of ARG. The objective of this work was to understand the impact of peri-natal antimicrobials on growth, mortality, fecal microbiota composition and abundance of antibiotic resistance genes using Illumina high throughput sequencing