Transcriptional profiling of germ-free and conventionalized mouse liver

The microbiome has been shown to have significant effects on susceptibility to liver disease. How the microbiome affects hepatic signaling pathways to mechanistically mediate these responses is unknown. Utilizing germ-free and conventionalized (microbiome-replete) mice, we characterized the effects of having a microbiome on the hepatic transcriptome. Germ-free C57BL/6 mouse littermates were separated at weaning (approx. 21 days). Half were maintained in sterile isolators, the other half were moved out of the isolators and housed in cages containing dirty bedding derived from elsewhere in the animal facility. After 3 weeks, the mice were sacrificed and liver was harvested and utilized for RNA sequencing by Illumina HiSeq 3000 system. 3 male and 3 female mice were analyzed for each condition (a total of 12 mice).