LAUSR

The objective of this study was to evaluate performance, diversity, composition, and predicted function of the intestinal microbiota of broilers raised under 3 different methods to induce necrotic enteritis (NE). The chicks in Experiments 1 and 2 were vaccinated against coccidiosis on day 1. Experiment 1: non-challenged and challenged birds were raised in floor pens with new litter and 58 birds/pen. The challenge consisted of Eimeria maxima inoculation on day 14 and Clostridium perfringens via water on days 18 to 19. Cecal microbiota was evaluated on days 18, 21, and 28. Experiment 2: non-challenged and challenged birds were raised in floor pens with recycled litter and 50 birds/pen. The challenge consisted of C. perfringens via feed from days 18 to 20. Ileal and cecal microbiota were evaluated on day 21. In Experiment 3, non-challenged and challenged birds were raised in battery cages with 8 birds/cage. Challenged birds were inoculated with E. maxima on day 14 and with C. perfringens on days 19 to 21. In the 3 experiments, ileal or cecal microbiota or both were analyzed through 16S rRNA sequencing. The performance of the birds was impaired in the 3 studies, regardless of the method used to induce NE. In Experiment 1, the microbiota did not significantly change across ages. In Experiment 2, α-diversity indices were lower in challenged vs. non-challenged birds in both ileal and cecal microbiota. The cecal microbiota composition and function was more affected than the ileal microbiota. In Experiment 3, Chao index (α-diversity) increased in challenged vs. non-challenged birds, and the composition of the ileal and cecal microbiota was not significantly affected. In conclusion, the overall feed conversion ratio was more affected in Experiment 3 (5.2, 11.1, and 30% for Experiments 1, 2, and 3, respectively), which also showed the highest degree of NE lesions. However, the largest variations of diversity and composition of the microbiota were observed in Experiment 2, when birds were raised in floor pens with reused litter, vaccinated against coccidiosis, and challenged with C. perfringens on days 19 to 21.