Mouse gut microbiomics of short chain fatty acid metabolism and mucosal responses

Summary The microbiota of the gastrointestinal (GI) tract plays a key role in the digestion of our food. The human gut microbiota can be studied using in vitro and animal models. In this thesis the mouse model is used to study the microbiota interaction with the diet and the host in different regions along the GI tract. These interacting microbes in the GI tract of humans and other mammals yield a wide range of metabolites, among which the short chain fatty acids (SCFA), in particular butyrate, acetate, and propionate, are the most abundant products of carbohydrate fermentation. Fermentable carbohydrates can modify the composition of the gut microbiota and change the SCFA concentrations in the gut. Opportunities for increasing specific SCFA by targeting their producers with carbohydrates are discussed. Five different fibres – resistant starch, inulin, fructooligosaccharides, arabinoxylan and guar gum – are tested for their modification of the mucosal tissue transcriptome, luminal microbiota composition and SCFA concentrations in the murine colon. The fibres inulin, fructooligosaccharides, arabinoxylan and guar gum led to increased SCFA concentrations and induced similar changes in relative abundance of microbial groups as determined by the MITChip, a phylogenetic microarray targeting the 16S ribosomal RNA of mouse intestinal microorganisms. Furthermore, these four fibres induced regulation of overlapping sets of genes in the mouse intestinal mucosa, where the transcription factor PPARγ was predicted to be a prominent upstream regulator of these processes. Multivariate data integration revealed strong correlations between the expression of genes involved in energy metabolism and the relative abundance of bacteria belonging to Clostridium cluster XIVa. Similar analyses were done for the caeca of the same mice, and were complemented with metatransciptome analyses. To comprehensively analyse RNAseq data of complex natural microbial communities, a de novo metatranscriptome assembly pipeline was developed and applied to unravel the activity profiles of the microbiota residing in the mouse cecum. This revealed distinct contributions of bacterial families to the fermentation of fibres into SCFA, involving the Bifidobacteriaceae, Lachnospiraceae, Clostridiaceae, Bacteroidaceae, Erysipelotrichaceae and Ruminococcaceae in some or all stages of the overall fibre fermentation activity. All families expressed genes encoding enzymes involved in the production of SCFA in different ratios. Specifically, butyrate producing bacteria correlated with a set of host genes involved in processes such as energy metabolism, transcriptional regulation and the mucosal immune system. In addition to complex carbohydrates, amino acids derived from dietary proteins can also serve as substrates for SCFA formation, leading to expansion of the fermentation end-product palet by including branched-SCFA. The long-term effects of high protein-diets on microbial community composition and activity were analysed. The caecal microbiota composition was changed by the high dietary protein. Most of the gene functions detected by metatranscriptomics in these caecal samples were assigned to the Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae. High protein diets induced a decrease of Lachnospiraceae activity, but stimulated the activity of the Erysipelotrichaceae, while the Clostridiaceae appeared to express the broadest range of amino acid metabolism associated pathways. In conclusion, this thesis describes dietary interventions to modulate the mouse intestinal microbiota and mucosa. The data provides expansion of the knowledge on interactions between the diet, microbiota and host. This information can be used to optimize the design and validation on dietary intervention studies in humans.