Transit kinetics and survival rates of a bacterial species from yoghurt (i.e. Streptococcus thermophilus strain FBI3) were examined in different digestive compartments of gnotoxenic and human-microbiota-associated mice. The production of the lactose-hydrolysing enzyme (i.e. beta-galactosidase) was also investigated within the digestive tract, using a chromosomal reporter system based on luciferase genes from Photorhabdus luminescens under the control of the plac promoter. In both mice models, S. thermophilus cells transited within 2 h from the stomach to the caecum-colon compartment of the digestive tract where they displayed a survival rate of nearly 100 %. In gnotoxenic mice, luciferase activity was found to increase in the second half of the small intestine and in the caecum-colon compartment when lactose was added to the drinking water provided to the animals. In human-microbiota-associated mice drinking lactose, luciferase activity was similarly increased in the second half of the small intestine but was drastically reduced in the caecum-colon compartment. This feature could be ascribed to the presence of the resident human microbiota.