Thanks to recent scientific progress a relationship between the intestinal microbiota and metabolic diseases could be established. A deeper understanding of underlying mechanisms has opened ways towards new approaches for alleviating conditions associated with metabolic diseases. Dysbiosis appears to be a major underlying factor associated with metabolic syndrome and related adverse health conditions. A major focus has therefore shifted to controlling of the gut microbiota through administration of functional lactic acid bacteria (LAB). The scope for health promotion and/or support by probiotics such as LAB has thereby been widened beyond the improving of intestinal health, also to include anti-obesity, anti-diabetic and cholesterol-lowering effects. In this study we investigated the cholesterol-lowering and microbiota modulatory potential of a LAB strain, Lactobacillus rhamnosus BFE5264, isolated from Maasai fermented milk. A mouse model receiving a high-cholesterol diet served as model for evaluating its functionality. The administration of L. rhamnosus BFE5264 resulted in a significant reduction of the serum cholesterol level that was accompanied by changes in intestinal microbiota and the production of short chain fatty acid (SCFA) in comparison to the control group. This strain also beneficially influenced the regulation of cholesterol metabolism in the liver in a pattern similar to that resulting from statin treatment, a drug inhibiting cholesterol biosynthesis in the liver.