Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics

Objectives Although taxonomic variations in chicken gut microbiota have been previously documented, their functional capacity remain poorly understood. To gain a better understanding, we incorporated whole genome shotgun metagenomics to analyse microbial communities of two different organs: the caeca and the large intestine. Results Using 24 samples obtained from the caeca and the large intestine of commercial chickens, we assembled Metagenome-Assembled Genomes (MAGs) and characterise their functional profiles. Afterwards, using 8 samples, we integrated this sequencing data with chicken performance metadata body weight (BW), weight gain, feed intake (FI), feed conversion ratio (FCR) and age. MAGs belonging to specific families were found to be positively associated with changes in performance parameters. Functional analyses suggest changes in nutrient geochemical cycles including hydrogen generation within the carbon-cycle. Furthermore, 108 CAZymes were identified for MAGs belonging to two major families – glycoside hydrolase (GH) and polysaccharide lyase (PL), which are important for breakdown of dietary carbohydrates and fibres. A total of 13 polysaccharide lyases were identified functioning on day 20 with enzymes were specific to organs. Overall, our results provide a deeper understanding of microbial-mediated metabolism concerning key performance parameters in chicken production.