Rearing system causes changes of behavior, microbiome, and gene expression of chickens.

It has been long demonstrated that cage rearing (CR) deprives the animal of the possibility to express natural behaviors and results in stress. However, the effect of the rearing system on gene expression and the molecular levels of the gut microbiome are unknown. 10-wk-old Beijing You chickens were studied in parallel CR and free-range (FR) systems for 30 wk, to investigate the effect of rearing systems on behavior, microbiota composition, and gene expression. From week 40, a match-mismatch design was conducted for 5 wk. The results indicated that CR deprives the animals of natural behaviors, evidenced by sham dust-bathing behavior. A decreased alpha diversity of gut microbiome composition of CR chickens was seen in FR compared to CR-FR chickens (P < 0.001), and the alpha diversity of gut microbiome composition of FR-CR was decreased as compared to FR chickens (P = 0.045). The heat map and beta-diversity analysis showed that the cluster of gut microbial compositions were similar between the mismatch groups (FR-CR and CR-FR), while those of CR showed the lowest diversity from the 4 groups. The relative abundance of gut microbes at genera and species levels was different between comparisons (P < 0.05). Moreover, the CR (both CR and FR-CR) triggered the downregulation of most Kyoto encyclopedia of genes and genomes pathways, while it was upregulated in 2 genetic information processing pathways, compared to FR hens regardless of long or short term. In conclusion, CR deprived chickens of their normal behavior and resulted in changes in the microbiome diversity and pathways and gene expression of chickens.