Because intestinal microflora play a pivotal role in the development of inflammatory bowel disease (IBD), there is currently some interest in alternating the composition of the microflora toward a potentially more remedial community. This paper summarizes the clinical and experimental efficacy of the manipulation of microflora by the use of antibiotics, probiotics, and prebiotics in IBD. Germinated barley foodstuff (GBF) is a prebiotic whose unique characteristics make it highly suitable for applications in IBD. It also helps prolong remission in remissive ulcerative colitis (UC) patients and also attenuates clinical activity in non-remissive UC patients. GBF has shown to be converted into a preferential nutrient, butyrate, for colonocytes through the action of Eubacterium and Bifidobacterium, and this bacterial butyrate can provide anti-inflammatory effects. The probiotic approaches for IBD include VSL#3, Nissle1917, Clostridium butyricum, and Bifidobacterium-fermented milk. In this paper, we summarize the distinctive role of another probiotic, Eubacterium limosum (E. limosum), which is a commensal microorganism that is promoted by GBF administration. The metabolites of E. limosum included butyrate, which can accelerate intestinal epithelial growth and inhibit IL-6 production. This new probiotic approach may be useful as an adjunctive IBD treatment in the future. Although these strategies hold great promise and appear to be useful in some settings, more experimental and clinical studies are needed to firmly establish their relevance.