Abstract Interactions between diet, microbiota and host response are important for intestinal health. Dietary fibers are known to promote intestinal health. Dietary fibers are edible plant-derived food components that encompass complex carbohydrates and lignin, resist the digestion in the small intestine of which some are degraded and fermented by gut microbiota in the large intestine, i.e. cecum and colon. The beneficial health effects of dietary fiber are suggested to be mediated by short-chain fatty acids (SCFA), which are produced by gut microbial fermentation. The underlying mechanisms of the interaction between dietary fiber, SCFA, and the host, however, are not in detail known. The objective of the research described in this thesis was to investigate the molecular effects and mechanisms underlying the effects of dietary fiber and its fermentation products, SCFA, in the large intestine. Firstly, the colonic transcriptional response to the main SCFA, acetate, propionate and butyrate, was investigated. SCFA were administered by rectal infusion in C57BL/6 mice fed a low fat/high carbohydrate (LFD) or high fat/low carbohydrate diet (HFD) and whole-genome gene expression analysis was performed on colonic scrapings by microarray technology. The analysis revealed specific and overlapping genes regulated between acetate, propionate and butyrate. In addition, gene response to SCFA was dependent on the diet, in particular for propionate. A set of propionate-regulated genes was activated on LFD while suppressed on a HFD and vice versa, indicating that diet composition is important factor in colonic response to SCFA. Secondly, the molecular effects of different dietary fibers and a control diet on the large intestine were investigated. Five different dietary fibers (inulin, fructo-oligosaccharide, arabinoxylan, guar gum, resistant starch) and a control diet were fed to C57BL/6 mice (10 days). The transcriptional response to the fermentable fibers was comparable in gene expression, microbiota composition, and luminal SCFA level in colon. In common for all fermented dietary fibers, the transcriptional regulator Pparg was identified as potential upstream regulator for the mucosal gene expression response. Moreover, bacteria mainly belonging to Clostridium cluster XIVa were found to correlate with mucosal genes related to metabolic, energy-generating processes. Next to common responses, analysis of the transcriptome revealed distinct responses of different dietary fibers. With respect to the cecal metatranscriptome, we identified distinct activities of bacterial families in the fermentation of dietary fiber. Moreover, using multivariate statistical analysis, we found correlations of the mucosal transcriptome with both the microbiota composition and metatranscriptome. In addition, we showed that SCFA, particularly butyrate and to a lesser extend propionate, transactivate PPARg and regulate the PPARg target gene Angptl4 in colonic cells. Thirdly, we tested the hypothesis that epithelial Pparg plays an important role in the fermentation of dietary fibers in the gut. Mice with an intestine-specific knock out (KO) of Pparg (cre-villin) and wild type (WT) mice were fed inulin (10 days). Whole-genome gene expression analysis of the colon revealed that diet had a larger effect than genotype on colonic, luminal microbiota composition, metabolome and mucosal transcriptome. We identified genes that were regulated by inulin in Pparg-dependent manner. In addition, we also identified genes regulated by butyrate in Pparg-dependent manner in organoids grown from colonic crypt cells derived from KO or WT mice. In conclusion, we identified distinct mucosal gene expression responses to the main fermentation products of dietary fiber, SCFA, on both low fat/high carbohydrate and high fat/low carbohydrate diet backgrounds. Dietary fibers induce common and specific effects in colon. Epithelial Pparg partially governs the response to fermentation of dietary fiber in colon. Next to the commonalties of dietary fiber for intestinal physiology, specific and differential effects were identified for microbial gene activity and composition as well as mucosal transcriptome response indicating that omics tools are useful in elucidating and dissecting effects of dietary fiber.