Effects of Dairy Matrix on the Intestinal, Liver, and Bone Transcriptome of Healthy Rats

Fermentation is one of the oldest food processing techniques and is widely utilized in dairy product processing, during which nutrient availability and bioactive compounds are altered. However, the complete mode of action by which fermented dairy exerts beneficial effects on the host remains unknown. The present study investigated the effect of milk and yogurt ingestion alone or combined with prebiotic inulin on the transcriptome of colonic mucosa, liver, and femur in healthy rats. Young growing male rats were fed one of four experimental diets containing (1) skimmed milk, (2) skimmed milk supplemented with inulin (5% <i>w</i>/<i>w</i>), (3) yogurt, or (4) yogurt supplemented with inulin (5% <i>w</i>/<i>w</i>) for 6 weeks. Microarray results revealed that yogurt consumption resulted in 2195 upregulated differential expressed genes (DEGs) and 1474 downregulated DEGs in colonic mucosa as compared with milk consumption. According to Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, tight junction-, immune system-related pathways in the colonic mucosa and metabolic pathways in the liver were enriched with yogurt consumption. No evident differences were identified in the bone transcriptome between the diet groups. In conclusion, the study found that the intake of fermented dairy exerts more pronounced effects on gene expression in the intestinal tissue than prebiotics supplementation.