A semi-continuous four-channel colon simulator was used to study the effects of lactose for the first time on the growth and fermentation dynamics of colonic microbiota. In six separate simulations, lactose supplementation increased the total SCFA concentration by 3-5 fold as compared with the baseline in the respective vessels. The total bacterial density was inversely correlated with lactic acid production (P = 0.003), while production of butyrate (P = 0.007) and propionate (P = 0.02) correlated with higher numbers of bacteria. A major shift in the microbial community structure in the lactose supplemented vessels was demonstrated by bacterial genomic %G+C-profiling of the total population, where lactose supplementation induced a clearly dominant peak in the bifidobacteria prominent area, %G+C 60-65. The transient shift to increased numbers of bifidobacteria (23-27%) of all bacteria in the first two vessels was also confirmed by the bifidobacteria-specific QPCR-method. In conclusion, lactose produced dramatic changes in microbiota composition and activity as compared with the baseline fermentation.