Altered egos: antibiotic effects on food animal microbiomes.

The human food chain begins with upwards of 1,000 species of bacteria that inhabit the intestinal tracts of poultry and livestock. These intestinal denizens are responsible for the health and safety of a major protein source for humans. The use of antibiotics to treat animal diseases was followed by the surprising discovery that antibiotics enhanced food animal growth, and both led to six decades of antibiotic use that has shaped food animal management practices. Perhaps the greatest impact of antibiotic feeding in food animals has been as a selective force in the evolution of their intestinal bacteria, particularly by increasing the prevalence and diversity of antibiotic resistance genes. Future antibiotic use will likely be limited to prudent applications in both human and veterinary medicine. Improved knowledge of antibiotic effects, particularly of growth-promoting antibiotics, will help overcome the challenges of managing animal health and food safety.