Schematic representation of the study design. Long-term antibiotic treatment (LAT) and short-term antibiotic treatment (SAT) trials were conducted in this study. Chickens were exposed to prophylactic antibiotic treatment from 1 to 21 dph in the LAT trial while 1 ~ 7 (1 W), 8 ~ 14 (2 W), 15 ~ 21 (3 W), and 22 ~ 28 (4 W) dph in the SAT trial. At 31 dph, all groups of chickens were infected with H9N2 AIV. Cloacal swabs were collected at seven time points, 4, 10, 16, and 25 dph (before H9N2 AIV infection) and 3, 7, and 11 dpi (after H9N2 AIV infection), to perform 16S rRNA sequencing. Cloacal swabs and intestinal content were collected at 25 and 31 dph to perform whole-metagenome shotgun sequencing, respectively. After H9N2 AIV infection, oropharyngeal swabs, cloacal swabs, and tracheal tissues were collected at 3, 5, and 7 dpi to determine viral titer.
