Identification of differential duodenal gene expression levels and microbiota abundance correlated with differences in energy utilisation in chickens

Among the terrestrial production animals, chickens are the most efficient users of energy. Apparentmetabolisable energy (AME) is a measure of energy utilisation efficiency representing the difference between energyconsumed and energy lost via the excreta. There are significant differences in the energy utilisation capability of individualbirds that have a similar genetic background and are raised under identical conditions. It would be of benefit to poultryproducers if the basis of these differences could be understood and the differences minimised. We analysed duodenal geneexpression and microbiota differences in birds with different energy utilisation efficiencies. Using microarray analysis,significant differences were found in duodenal gene expression between high- and low-AME birds, indicating that level ofcell turnover may distinguish different groups of birds. High-throughput sequencing of bacterial 16S rRNAgenes indicatedthat duodenal microbiota was dominated by Lactobacillusspecies and two operational taxonomic units, identified aslactobacilli species, were found to be more abundant (P<0.05) in low-AME birds. The present study has identified geneexpression and microbiota properties that correlate with differences in AME; further studies will be required to investigatethe causal relationships.