In poultry farming, antibiotics are known to control disease and improve growth performance. But a new study shows that the timing and duration of antibiotic administration can have adverse effects. Although not statistically significant, long-term (3 weeks) use of the antibiotic enrofloxacin was found to slow the growth rate of chickens, while short-term (1 week) antibiotics increased the growth rate. Interestingly, however, short-term antibiotics usage provided an opportunity for an increase in the abundance of opportunistic pathogens and increased virus numbers after infection with H9N2 avian flu. These effects were linked to disturbances in the gut microbiota, with both long- and short-term antibiotics expanding the pool of antibiotic resistance genes harbored by chicks, posing a potential threat to public health. These findings highlight the harmful effects of prophylactic antibiotics in poultry farming, and should encourage more cautious use of antibiotics in animal management.