Lactobacillus plantarum is a common inhabitant of mammalian gastrointestinal tracts and specific strains belonging to this species are marketed as probiotics intended to confer beneficial health effects. To assist in determining the physiological status and host-microbe interactions of L. plantarum in the digestive tract we assessed changes in the transcriptome of L. plantarum WCFS1 during colonization of the cecum of germ-free mice. According to the transcript profiles L. plantarum WCFS1 was metabolically active and not under severe stress in this intestinal compartment. Carbohydrate metabolism was the most strongly affected functional gene category whereby many genes encoding diverse sugar transport and degradation pathways were induced in mice even compared to L. plantarum grown in a mouse chow-derived laboratory medium. This suggests that the ability of L. plantarum WCFS1 to consume diverse energy sources including plant-associated and host-derived carbohydrates was increased during its residence in the digestive tract. Many of these genes were also induced in L. plantarum colonizing germ-free mice fed a humanized Western-style diet. Similarly a core set of genes encoding cell surface-related properties were differentially expressed in mice. This set includes genes required for the D-alanylation and glycosylation of lipoteichoic acids that were strongly down-regulated in mice. In total L. plantarum exhibits a distinct in vivo transcriptome directed towards adaptation to the mouse intestinal environment.