Recent development and application of next-generation sequencing technologies using 16S rRNA gene have allowed investigating the significant roles of microbiota in the gastrointestinal tract and facilitated the investigation of host–pathogen interaction and the role of the intestinal microbiota in diseases. Inflammation in the intestine is often associated with alteration of intestinal microbiota homeostasis. Several studies reported that mixed Eimeria infection causes an alteration of intestinal microbiota community in broilers fed dietary supplement such as essential oils, probiotics or dietary fish meals. However, there have been no reports to observe the distribution of gut bacterial communities and identification of specific OTU before/after feeding dietary phytonutrients in 3 commercial broiler breeds to an infectious NE challenge with E. maxima/C. perfringens. Therefore, the current study was undertaken to determine whether dietary supplementation with a mixture of oleoresins from Capsicum/Curcuma longa might potentiate NE disease resistance in Cobb, Hubbard, and/or Ross chickens, and if so, to elucidate the intestinal microbiota of 3 commercial broilers in depth by using the
high-throughput pyrosequencing and provide a better insight into the microbial communities and diversity in 3 groups; 1) unsupplemented and uninfected (control), 2) unsupplemented and E. maxima/C.perfringens co-infected (NE), 3) Capsicum/Curcuma longa oleoresin supplemented
and co-infected (NE + XT). This is the first study to show significant dietary effect of phytonutrients (C. annuum and C. longa) on genetically selected commercial broiler breeds to NE and associated with intestinal microbiota.