The effects of digestion resistant carbohydrates on the colon microbiota and colon tissue transcriptome of weanling rats

Digestion-resistant carbohydrates (DRC) in the diet pass to the terminal ileum and large bowel where they may be fermented by resident bacteria. The bacterial communities in the bowel of young animals undergo dramatic shifts in composition following weaning. These compositional and associated biochemical changes may have long-lasting impacts on the host. However, the mechanisms by which diet induced changes in the microbiota influence host physiology requires further investigation. This study examined whether bacterial community compositions could be engineered by supplementing the diet of newly-weaned rats with different forms of DRC and the subsequent effects these altered microbial communities had on host physiology. Newly weaned conventionally raised or germ-free male 21-28 day old Sprague-Dawley rats were fed a basal diet or basal diets supplemented with DRC at concentrations up to 5% for 14 or 28 days. Colonic digesta was collected from each rat for analyses to determine short chain fatty acid (SCFA) concentrations and to compare bacterial community structure by temperature gradient gel electrophoresis (TTGE) and 454 pyrosequencing analysis of the V3 hypervariable region of the 16S rRNA gene. DRC induced alterations in the host transcriptome were assessed by microarray analysis of RNA extracted from colon tissue. Feeding DRC significantly increased concentrations of SCFA in the colon digesta of young rats. The DRC induced changes in SCFA concentrations were also accompanied by alterations in the colonic microbiota structure. Each type of DRC altered the microbiota in a distinctive manner, which could be clearly differentiated from those of rats fed the basal diet. Feeding DRC also resulted in more uniform microbiota compositions compared to the basal diet. The alterations in microbiota composition were associated with changes in host colon gene expression profiles. Each form of DRC altered colonic gene expression in a distinct manner with profiles from rats fed the same diet showing greater similarity than those fed different diets. Differentially expressed genes in the colon were involved in a number of biological functions including energy metabolism, immune function, and cellular growth and differentiation. Comparisons of the effects of DRC on host gene expression between conventionally raised and germ-free rats showed that the resident microbiota was a determining factor of the host response to DRC. Feeding DRC to conventionally raised rats resulted in the differential expression of different sets of genes compared with feeding DRC to germ-free rats. The results of this study show that the bacterial communities in the colon of newly-weaned rats can be engineered by supplementing the diet with DRC. Using this approach, unique bacterial communities with enhanced fermentative capacity, increased uniformity, and distinct effects on host gene expression were selected. The findings from this study provide support and future scope for the development of different dietary supplements that target different parameters of large bowel function