Purpose: This study assessed the gut microbiome and concurrent prevalence of Salmonella spp. and Campylobacter spp. in the cecum and ileum of broilers.
Methods: A longitudinal study (hatch to market, day 42) was conducted to assess the gut microbiome and prevalence of Salmonella spp. and Campylobacter spp. in the cecum and ileum of chicks. Three diets, with and without bacitracin dimethyl salicyclate-50, were provided to the birds from day 0 to day 22 (starter diet), day 23 to day 35 (grower diet), and day 36 to day 42 (finisher diet). Cecal, ileum, litter, and feed samples were collected and sequenced using Illumina MiSeq.
Results: Firmicutes was the most abundant phylum in both cecum and ileum. The proportion of Firmicutes in the cecum decreased, gradually, with bird age (75.5% to 42.1% from day 0 to 42). Proteobacteria were abundant (18.8%) in the cecum at day 0, but varied in abundance with age. Enterococcus spp. was abundant in both the cecum and ileum on day 0, but decreased with age, from 54.0% to <1.0%. Day, diet, and treatment interaction (P≤0.0001) was significant for most genera, except members of the orders Clostridiales and Lactobaccillales. The prevalence of Salmonella spp. and Campylobacter spp. varied from 16.7 to 100.0% and 0 to 66.7%, respectively, in the cecum and ileum. Prevalence of Salmonella spp. and Campylobacter spp. in litter was 41.7% and 25.0%, respectively. Broiler age, diet, and treatment (control vs. antibiotic supplemented feed) affected the bacterial taxa in the gut.
Significance: The results of this study provided insight on the impact of antimicrobial supplementation in the feed on gut microbial composition and foodborn pathogen prevalence.