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. β-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 2h 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.