Transcriptomic, untargeted metabolomic, and gut microbiota studies on the anticoccidial activity of the combination formula in broilers

Coccidiosis, a devastating intracellular parasitic disease, poses a significant threat to the poultry industry. Traditional control methods, which involve the inclusion of anticoccidial drugs in feed, have raised concerns over veterinary drug residues. Consequently, there is a pressing need to identify suitable alternatives or complementary strategies to anticoccidial drugs, with plant-derived natural products emerging as a promising candidate. Our laboratory has previously identified a combination formula that demonstrates good anticoccidial activity. However, the underlying mechanisms remain elusive. This study aims to elucidate the mechanism of action of this formula using a multi-omics approach, including transcriptomics, untargeted metabolomics, and gut microbiota analysis. Cecal transcriptomic analysis revealed significant enrichment in pathways, such as lysosomes, ribosomes, oxidative phosphorylation, and sphingolipid metabolism following treatment with the combination formula. Untargeted metabolomic profiling indicated a pronounced enrichment in the gut IgA generation immune network pathway, with retinoic acid identified as a key differential metabolite. Gut microbiota sequencing analysis suggested that the combination formula modulates the gut microbiota of infected broilers towards a composition resembling that of healthy broilers. Collectively, these results suggest that the combination formula exerts its anticoccidial effects through the regulation of differential gene clusters, metabolites, and microbiota. The results of this study have provided us with a deeper understanding of the good anticoccidial effects of the combination formula. IMPORTANCE Eimeria tenella is a significant parasitic protozoan that poses a substantial threat to the development of the poultry industry. The combination formula, a synergistic blend of plant-derived natural products, has been identified in our laboratory for its good anticoccidial effects. In this study, we employed non-targeted metabolomics, transcriptomics, and gut microbiome sequencing to elucidate the mechanism of action against coccidiosis. Our results revealed a multitude of differential gene clusters and metabolites. Furthermore, the gut microbiota structure of the cecal content in the treated group more closely resembled that of the healthy control group.