Effects of anti-coccidial vaccination and exogenous enzymes on chicken growth performance and gut health

Gut health is the relationship between the host, gut microbes and diet. Therefore, comprehensive analyses of the host immune system, microbiota and diets in the same setting are required in order to study gut health. Correlations between the host immune system and the gut microbiota could provide a better understanding of the relationship between host and microbes. Knowledge of the relationships between the intestinal immune system and microbiota could help producers improve poultry health and nutrient utilisation. Application of this knowledge could result in better poultry growth performance, animal welfare and reduced environmental impact. Two by two factorial arrangement study was conducted using Ross 308 broiler chickens. Anti-coccidial vaccination against Eimeria protozoa was used as a factor to create gut-damaged chickens. Combination of protease, xylanase and beta-glucanase enzymes was used as a dietary intervention factor. Chicken growth performance was significantly affected by the vaccination while enzymes supplement significantly improved the feed conversion ratio. Although coccidiosis lesions were observed in non-vaccinated chickens at 24-day-old, the feed efficiency of non-vaccinated chickens still outperformed the vaccinated chickens at this period. While at 35 days of age, vaccinated chickens showed compensatory growth with significantly better growth performance than non-vaccinated chickens. Therefore, samples for correlation analysis were selected from 24-day-old rather than 35-day-old chickens. Using 16S rRNA metabarcoding analysis, the abundances of eleven bacterial genera at the ileum of 24-day-old chicken were significantly affected by the vaccination where two bacterial genera were significantly affected in the caecum. Although the enzymes supplement did not significantly affect the microbiota population at both ileum and caecum from 16S rRNA metabarcoding analysis, functional analysis using shotgun metagenomics and Carbohydrate Active enzymes database (CAzy) showed significant alteration by the enzymes supplement. From transcriptomic analysis, vaccination significantly affected the expression of 96 and 46 genes at the ileum and caecum respectively. In contrast, 4 and 3 genes were differentially expressed between the enzymes and non-enzymes supplement chicken at the ileum and caecum respectively. At both ileum and caecum, several immune-related genes were up-regulated while multiple absorption-related genes were down-regulated in vaccinated chicken. Interestingly, with more differentially expressed genes at the ileum than the caecum, no Gene Ontology (GO) term was significantly enriched at the ileum when compared between vaccinated and non-vaccinated chicken. Correlation between gut microbiota and gene expression using Weighted Gene Co-expression Network Analysis (WGCNA) showed multiple significant correlations between gene clusters and bacterial taxa. Using differentially expressed gene results from the RNA-seq analysis, 84 and 191 significant correlations were identified at ileum and caecum respectively. In conclusion, anti-coccidial vaccination had a significant impact on chicken growth performance, gut microbiota and intestinal immune response. Alteration of the nutrition using exogenous enzymes improved feed efficiency with minor impact on the gut microbiota and host response. Correlation between gut microbiota and intestinal gene expression were identified. These bacteria and genes could be used as potential markers for gut health however, further investigation using these findings is required