16S rRNA amplicon sequences were extracted from the ileum and cecum of two genetically different broilers (slow-growing (SG) and conventional (CONV)) 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 (ST) via oral gavage while the rest were given an oral gavage of saline control (C). 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.

The experimental unit was isolator with an exception for samples collected on day 7 in which each chick represented its own independent data point (N = 48, 24 SG and 24 CONV). Forty-eight samples were still collected for each of the remaining days of the experiment but because two birds of the same breed were sampled from each isolator, they were handled as replicates and their data was merged as a single point resulting in N = 24 on days 13, 17, 21 and 24. In this study, we did not have an isolator in which both replicates sampled on the same day were ‘lost’ and therefore 24 data points were collected in all 4 of the remaining days.

The listed samples below (N = 14 total) are mising from the analysis due to having too low of microbial biomass to be detected by the sequencer:

1. sample 41 (Ileal, D7, SG, C, from co-housing)
2. sample 42 (Ileal, D7, SG, C, from co-housing)
3. sample 43 (Ileal, D7, SG, C, from co-housing)
4. sample 44 (Ileal, D7, SG, C, from co-housing)
5. sample 45 (Ileal, D7, SG, C, from co-housing)
6. sample 46 (Ileal, D7, SG, C, from co-housing)
7. sample 47 (Ileal, D7, SG, C, from co-housing)
8. sample 48 (Ileal, D7, SG, C, from co-housing)
9. sample 73 (Ileal, D13, CONV, C, from Isolator 13)
10. sample 76 (Ileal, D13, SG, C, from Isolator 14)
11. sample 78 (Ileal, D13, CONV, C, from Isolator 15)
12. sample 88 (Ileal, D13, CONV, C, from Isolator 20)
13. sample 89 (Ileal, D13, SG, C, from Isolator 21)
14. sample 174 (Cecal, D21, CONV, ST, from Isolator 15)