Dynamic Structural and Functional Changes of the Chicken Intestinal Microbiome in Response to Necrotic Enteritis

To elucidate the effects of Eimeria and C. perfringens on gut microbial composition and function in the context of NE, and to characterize dynamic changes in the gut microbiota during NE development, two independent chicken NE trials were conducted. In each trial, NE was induced by sequential challenges with Eimeria maxima and C. perfringens on days 11 and 15, respectively. In the first trial, ileal and cecal digesta were collected on day 18 and subjected to 16S rRNA sequencing to study bacterial structural changes. Additionally, cecal samples underwent metagenomic sequencing for functional analysis. In the second trial, ileal and cecal digesta were collected on days 12, 15, 16, 17, and 18 and analyzed using 16S rRNA sequencing to monitor bacterial dynamics throughout NE development.