Cecal microbiome in broiler chicken related to antimicrobial feeding and bird's sex.

This study investigated the cecal microbiome of broilers raised under specific antimicrobial feeding programs (AFPs). A total of 2304 day-old Ross-708 male (M, n = 1152) and female (F, n = 1152) chicks were distributed into 48 floor pens which were allocated to one of three AFPs: Conventional, raised without medically important antibiotics (RWMIA), and raised without antibiotics (RWA). At 28 (D28) and 41 (D41) days of age, cecal contents were collected for culture dependent and independent analyses. At both 28 and 41 days, Enterococcus was more abundant in RWA-raised broilers than other groups with the most abundance of this bacterium being found in female birds (P < 0.05). At D41, the most abundant Eimeria tenella counts was observed in RWA-raised broiler ceca (P < 0.05). Sex effects were observed on the abundances of four of the 248 identified antimicrobial resistance genes while abundances of 10 were modulated by AFPs (P < 0.05). Ceca of females birds showed more tssB than males, and ceca of RWMIA-raised birds contained the highest abundance of chuY genes regardless of sex. This study showed that in a specific feeding program, cecal resistome can be affected by chicken's sex contributing to understand the AMR related to the AMU.