Metagenomes of feces collected from pigs reared in organic, antibiotic-free and penicillin-using settings

Antimicrobial resistance is a recognized public health crisis that requires mitigation on numerous fronts along the One Health continuum. With the bulk of antimicrobials being administered to livestock, producers are under pressure to modify their husbandry practices towards reducing antimicrobial usage. Consequently, products from farms that are certified antibiotic-free and organic are increasing in market share. The goal of this study was to evaluate the impact of rearing practices on the fecal microbiota composition and resistome of pigs. The sampled antibiotic-free farms complied with three types of certifications, namely Organic, Certified-Humane and AGRO-COM. As a control group in the same geographical location, we sampled a conventional farm that uses prophylaxis penicillin for farrowing sows and piglets. The specific goals were to evaluate the impact of husbandry practices and animal age on gut microbiome, resistome and mobilome composition and structure, assess the contribution of microbiome composition on the resistome, identify antimicrobial resistance genes relevant to food safety and clinical settings, predict antimicrobial resistance genes of importance in distinguishing between organic, antibiotic-free and conventional settings. It is not uncommon in the literature to encountered articles in which the authors use the 'raised without antibiotics' appellation to refer to pigs that are not subjected to in-feed antibiotics at weaning, but that do received antibiotics during their lifetime. In the present study, RWA is used for pigs that did not receive any antibiotic from birth to slaughter, and for their mother sows that did not receive any antibiotics since they were transferred as gilts from reproduction farms to maternity wards. It is unique as it used a longitudinal approach to assess two types of truly RWA practices, including one certified organic, on the microbiome and resistome of pigs.