Temporal changes in jejunal and cecal microbiome of broiler chickens with clinical coccidiosis (Eimeria maxima)

Authors: Miska, Kate; Campos, Philip; CLOFT, SARA - Purdue University; Jenkins, Mark; Proszkowiec-Weglarz, Monika

Submitted to: Agriculture Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/8/2024
Publication Date: 10/15/2024
Citation: Miska, K.B., Campos, P.M., Cloft, S.E., Jenkins, M.C., Proszkowiec-Wegla, M.K. 2024. Temporal changes in jejunal and cecal microbiome of broiler chickens with clinical coccidiosis (Eimeria maxima). Agriculture Journal. 14(20), 2976. https://doi.org/10.3390/ani14202976.
DOI: https://doi.org/10.3390/ani14202976

Interpretive Summary: Coccidiosis is one of the most prevalent diseases affecting broiler (meat) chickens worldwide which causes economic losses because infected chickens grow more slowly and less efficiently than healthy ones. Coccidiosis is caused by a parasite Eimeria (at least seven species) which infects the gastrointestinal tract of the chicken. The infection causes diarrhea, inappetence, and in some cases death. The goal of the current study was to determine changes in the bacteria in the jejunum and ileum (small intestine) following infection with Eimeria maxima. Intestinal samples were taken at 0, 3, 5-, 7-, 10-, and 14-days post infection. The experimental infection resulted in a decrease in body weight gain, increase in feed conversion ratio, compromised gut morphology, decreased plasma carotenoid levels (indicative of a leaky-unhealthy intestine). The intestinal bacteria content was determined by sequencing a portion of the 16s rDNA gene. Our results indicate that infection affected the diversity within and between bacterial particularly at the height of infection. In samples from infected birds, species of bacteria that can be opportunistic pathogens were more abundant than in healthy birds. In uninfected birds, bacteria which produce short chain fatty acids and are associated with improved growth were more abundant compared to infected birds. In conclusion, E. maxima affects the ecology of the small intestine by disrupting its morphology and integrity and also skews the types of bacteria present, to those that could be opportunistic pathogens. Coccidiosis is a complex gastrointestinal disease and understanding its effects on the host will help find effective control methods in the future.

Technical Abstract: Coccidiosis in broiler chickens continues to be a major disease of the gastrointestinal tract, causing economic losses to the poultry industry worldwide. The goal of this study was to generate a symptomatic Eimeria maxima (1,000 oocysts) infection to determine its effect on the luminal and mucosal microbiome populations (L and M) in the jejunum and ileum (J and IL) from day 0 to14 post-infection by sequencing of 16s rRNA using Illumina technology. Infected birds had significantly (p<0.0001) lower body weight gain (BWG), higher feed conversion ratio (FCR) (p=0.0015), increased crypt depth, and decreased villus height (p<0.05). The significant differences in alpha and beta diversity were observed primarily at height of infection (D7). Analysis of taxonomy indicated that J-L and M were dominated by Lactobacillus, and in IL-M, changeover from Candidatus Arthromitus to Lactobacillus as the major taxon was observed, which occurred fast in infected animals. LefSE analysis found that in the J-M of infected chickens Lactobacillus was significantly more abundant in IF chickens. These findings show that E. maxima infection affects the microbiome of the small intestine in a time-dependent manner, with different effects on the luminal and mucosal populations.