Transcriptomic and epigenomic analysis of germ-free and colitic mice

The gut microbiota influences host epigenetics by fermenting dietary fiber into butyrate. Although butyrate could promote histone acetylation by inhibiting histone deacetylases, it may also undergo oxidation to acetyl-CoA, a necessary cofactor for histone acetyltransferases. Here, we find that epithelial cells from germ-free mice harbor a loss of histone H4 acetylation across the genome except at promoter regions. Using stable isotope tracing in vivo with 13C-labeled fiber, we demonstrate that the microbiota supplies carbon for histone acetylation. Subsequent metabolomic profiling revealed hundreds of labeled molecules and supported a microbial contribution to host fatty acid metabolism, which declined in response to colitis and correlated with reduced expression of genes involved in fatty acid oxidation. These results illuminate the flow of carbon from the diet to the host via the microbiota, disruptions to which may affect energy homeostasis in the distal gut and contribute to the development of colitis. Overall design: RNA-seq and ChIP-seq for H4ac4 were performed on colonic epithelial cells isolated from germ-free or conventional mice (n = 5 for RNA-seq, n = 2 for H4ac4 ChIP-seq and corresponding input chromatin). The H4ac4 ChIP-seq included an exogenous spike-in of Drosophila chromatin for reference normalization. RNA-seq was also performed on whole colon and cecal tissue from mice with or without DSS-induced colitis and treated with isotope-labeled or unlabeled inulin (n = 3).