Temporal dynamics of cecal microbiota composition and diversity in broiler chickens challenged with different doses of Eimeria spp.

Abstract

Coccidiosis, caused by Eimeria spp., is one of the major enteric diseases affecting broiler chickens, compromising gut integrity and altering gut microbiota composition. This study aimed to evaluate the effects of different Fortegra® Eimeria spp. challenge doses on the composition and diversity of the cecal microbiota over time postinfection. Broiler chickens were allocated into three groups: a control group receiving PBS, G1 challenged with a 10 × vaccine dose, and G2 challenged with a 20 × vaccine dose. Cecal content samples were collected at 7, 14, and 21 days post-inoculation and analyzed using 16S rRNA next-generation sequencing (NGS). Across all groups, the dominant bacterial phyla were Firmicutes and Bacteroidota. A transient increase in Proteobacteria was observed at 7 days postinfection, suggesting an early phase of microbial instability. Taxonomic shifts indicated an initial disruption of the cecal microbiota, followed by progressive microbial reorganization over time. Alpha diversity analysis revealed marked temporal changes in both G1 and G2, with increased richness and diversity at later time points, consistent with a process of microbial succession. In terms of beta diversity, Jaccard distance analysis demonstrated temporal shifts in taxa presence and absence. G1 exhibited a pronounced temporal pattern characterized by continuous species turnover, whereas G2 showed a constrained temporal shift with indications of progressive stabilization. Overall, the findings suggest that temporal dynamics exert a greater influence than challenge intensity in shaping the gut microbiota, reflecting a succession process associated with the partial restoration of gut homeostasis.