The Impact of Broiler Genetics and Salmonella Exposure on the Ileal and Cecal Microbiome

16S rRNA amplicon sequences were extracted from the ileum and cecum of two genetically different broilers (slow-growing and conventional) across 5 different time points (Day 7, 13, 17, 21, and 24). Broilers were co-housed together from day 0 to day 7. A total of 48 chicks were sacrificed and their ileal and cecal contents were collected on day 7 (N = 24/breed). After sampling on day 7, the broilers were moved to a new facility where they were separated into isolators (4 rooms, 6 isolators/room, 11 chicks of each breed/isolator). Two chicks per isolator were sacrificed and sampled for their ileal and cecal contents on the 13th day. On day 14 of the experiment, two out of the four rooms were randomly chosen and birds in those two rooms were challenged with 1x10^8 /ml Salmonella Typhimurium via oral gavage while the rest were given an oral gavage of saline control. Samples were collected again on days 17, 21, and 24 (N = 48 total, 24 per breed). The purpose of this experiment is to identify and characterize the relationship between Salmonella enterica ser. Typhimurium challenge and genetic lines of selected broiler species on the ileal and cecal microbiome.