Effect of fermentation and prebiotic supplementation on organs of healthy rats

The data was used to investigate how milk and yogurt ingestion alone or combined with prebiotic inulin influences the colonic mucosa, liver, and bone transcriptome. A 6-week dietary intervention was conducted in healthy young growing male rats which received a diet containing: 1) milk, 2) milk supplemented with inulin (5% w/w), 3) yogurt, or 4) yogurt supplemented with inulin (5% w/w).
The 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 GO categories and 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. Overall, the study found that intake of fermented dairy exerts more pronounced effects on gene expression in the intestinal tissue than prebiotics supplementation.
DNA microarray data (File Bone_, Gut_, and Liver_FDR_0.1 tacx) can only be reached using a software called Transcriptome Analysis Console.
From a direct comparison of the Milk and Yogurt groups, 2195 upregulated DEGs and 1474 downregulated DEGs were identified in CMS (List of differential expression genes)
To support the transcriptomic analyses, real-time PCR was performed on three selected genes (q-PCR result). The results showed that, although non-significant, the mRNA expression level of Arhgef18 was higher for the Yogurt group, consistent with transcriptomic analysis.