Metagenomic Insight into Cecal Microbiota Shifts in Broiler Chicks Following Eimeria spp. Vaccination

Coccidiosis, caused by <i>Eimeria</i> spp., remains a major challenge in poultry production, significantly affecting poultry health and performance, leading to substantial economic losses. While its impact on gut health is well documented, the interplay of <i>Eimeria</i> spp. challenge and/or vaccination with the intestinal microbiota remain insufficiently understood. Therefore, the aim of this study was to investigate the effects of <i>Eimeria</i> spp. (<i>E. acervulina</i>, <i>E. maxima</i>, and <i>E. tenella</i>) challenge, alone or in combination with a commercially available vaccine, on broiler performance, intestinal gross lesions, and cecal microbiota structure and function in experimentally challenged broiler chicks. A total of 216 Ross 308^® broilers were randomly divided into three groups, with six replicates per group, according to the following experimental design: (A) negative control, (B) <i>Eimeria</i> spp.-challenged birds on day 16, and (C) <i>Eimeria</i> spp.-vaccinated and -challenged birds. Performance parameters were recorded on a weekly basis, coccidiosis gross lesions in the intestine were evaluated on days 23 and 29, and microbiota samples were collected on day 23. Broilers in the challenged group exhibited significantly (<i>p</i> ≤ 0.05) increased coccidiosis gross lesions in the intestine at both sampling periods (7 and 19 days post-infection, dpi), whereas vaccination significantly (<i>p</i> ≤ 0.05) minimized the severity of lesions at both time points. The challenged-only group showed significantly (<i>p</i> ≤ 0.05) lower average daily weight gain (ADWG) during the finisher phase and the overall experimental period compared to the vaccinated group. Additionally, average daily feed intake (ADFI) during the post-challenge period (22-29 dpi) was significantly (<i>p</i> ≤ 0.05) reduced in both challenged groups. Alpha diversity decreased in the challenged (<i>p</i> = 0.016) and vaccinated-challenged (<i>p</i> = 0.016) groups compared to control, Accordingly, beta diversity was reduced in groups B and C compared to the control group. This reduction was accompanied by an increased relative abundance of Proteobacteria (18, 71% in Group B and 10, 87% in Group C) and potentially pathogenic genera (<i>Escherichia</i> spp. and <i>Shigella</i> spp. <i>p</i> < 0.05), along with a decline in short-chain fatty acid (SCFA)-producing bacteria (<i>Oscillibacter</i> spp. and <i>Eisenbergiella</i> spp.) in groups B and C, respectively, compared to the control. Predictive functional metagenomics indicated disruptions in amino acid metabolism, nucleotide degradation, and lipid metabolism, potentially affecting gut integrity and nutrient absorption. Additionally, in the vaccinated group, gross lesions in the intestine were reduced in severity and microbial diversity was partially preserved, resulting in a microbiota composition more similar to that of the control group. Overall, these findings support that <i>Eimeria</i> spp. infection alters gut microbiota and function in broiler chicks, underscoring the need for further research into alternative strategies, such as probiotics and phytobiotics, to support gut health and disease resilience in poultry.