Probiotics, prebiotics and combinations thereof, i.e. synbiotics, have been reported to modulate gut microbiota of humans. In the present study effects of a novel synbiotic on the composition and metabolic activity of human gut microbiota were investigated. Healthy volunteers (n =18) were enrolled in a double-blinded, randomized, placebo-controlled crossover study and received synbiotic (Lactobacillus acidophilus NCFM (10(9) CFU) and cellobiose (5g)) or placebo daily for three weeks. Fecal samples were collected and lactobacilli numbers were quantified by qPCR. Furthermore, 454 tag encoded amplicon pyrosequencing was used to monitor the effect of synbiotic on the composition of the microbiota. The synbiotic increased levels of Lactobacillus spp. and relative abundances of the genera Bifidobacterium, Collinsella and Eubacterium while the genus Dialister was decreased (p < 0.05). No other effects were found on microbiota composition. Remarkably, however the synbiotic increased concentrations of branched-chain fatty acids, measured by gas chromatography, while short-chain fatty acids were not affected. This article is protected by copyright. All rights reserved.